Re: [galaxy-user] tophat issues
Hello Miro, It sounds like perhaps the datatype is not being assigned correctly, which may mean that they quality scores are not scaled properly. To double check both, see the instructions in our wiki here: http://wiki.galaxyproject.org/Support#Dataset_special_cases If you still need help after this, please write back to share a history, Best, Jen Galaxy team On 11/29/13 5:49 AM, miroslav.sotak wrote: To whom it may concern I do have a problem with tophat. I can easily put fastq data to history and according to RNA-seq Analysis Exercise provided by Jeremy. We checked the type of Ascii ofset for the quality estimation. I tried even quality data converter set to 33 (we do have data of this ASCII offset from 2 different sources) but tophat for Illumina simply can not read the data before and even after quality format converter. We do not have any idea what is going on. I am logged in Galaxy with current email, can you check my data and is there any converter for quality offset? Sincerely Miro Sotak ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-user] tophat issues
To whom it may concern I do have a problem with tophat. I can easily put fastq data to history and according to RNA-seq Analysis Exercise provided by Jeremy. We checked the type of Ascii ofset for the quality estimation. I tried even quality data converter set to 33 (we do have data of this ASCII offset from 2 different sources) but tophat for Illumina simply can not read the data before and even after quality format converter. We do not have any idea what is going on. I am logged in Galaxy with current email, can you check my data and is there any converter for quality offset? Sincerely Miro Sotak ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-user] Tophat/Cuff parameters
Hello, Yes, this is correct, not all parameters can be adjusted in the UI. Many can, especially with Tophat, but not all. The list of implemented parameters that will match the documentation is listed at the bottom of each of these tools. The UI form itself up top may have a slightly different human readable name, but most will include the parameter name -r, etc. To see all of the parameters on the forms: 1. Tophat/2 - open TopHat settings to use: Full parameter list 2. Cufflinks/merge/compare/diff - open or modify any listed on form to see full content This tool is in the Tool Shed (http://usegalaxy.org/toolshed), so if you had programming resource available, then these could certainly be modified. Development questions can go do the galaxy-...@bx.psu.edu mailing list, but really the best place to start is in our wiki: http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax http://wiki.galaxyproject.org/Tool%20Shed It would be really helpful if you sent questions directly to the galaxy-u...@bx.psu.edu mailing list going forward. Thanks, Jen Galaxy team On 11/14/13 1:08 PM, Irene Bassano wrote: Hi Jen, thanks a lot for your reply. I am trying to apply some changes to certain parameters in cufflinks. I have read them on the manual but on galaxy are not all listed. is this because they have been chosen already by galaxy and set to certain values you guys believe are optimal? I cannot find for example: Maximum genomic length allowed for a given bundle. Minimum intron size allowed in genome. Minimum average coverage required to attempt 3' trimming. and many others. I also wanted to access full parameters for Tophat and Cuffdiff... Any suggestion on how can I access them? Thanks, Irene -- Jennifer Hillman-Jackson http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-user] Tophat for Illumina - built-in dog genome mislabelled
Hi, I minor annoyance that I had found with the current implementation of Tophat for Illumina (version 1.5.0) in the public usegalaxy.org site: When you submit sequences for alignment, the dropdown list of available genomes gives 2 dog genome choices - BUT both are labeled the same - Dog(Canis lupus familiaris): canFam2. After trial and error I found that the second (lower on the list) choice is actually Dog(Canis lupus familiaris): canFam3.1. Hopefully this can be corrected at some point - maybe when the next release comes out from the Broad. Michael [cid:image002.png@01CEC5C0.75D35560] Michael H. Court, BVSc, PhD, Diplomate ACVA Professor and William R. Jones Endowed Chair Individualized Medicine Program Pharmacogenomics Laboratory Department of Veterinary Clinical Sciences College of Veterinary Medicine, Washington State University 100 Grimes Way, Pullman, WA 99164-6610 Office: 509-335-0817 Cell: 774-287-7082 Fax: 509-335-0880 michael.co...@vetmed.wsu.edumailto:michael.co...@vetmed.wsu.edu www.vetmed.wsu.eduhttp://www.vetmed.wsu.edu/ inline: image002.png___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-user] TopHat
Hi all, I am trying to perform TopHat for Illumina from Galaxy's Main Server, and it is in queue for the past 3 to 4 days. Is this normal? Thanks Regards,Kumar. ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] TopHat
Hello Kumar, The NGS queue has been down for several days now. We expect this to be up soon. This is related to the upgrades on the public Main server, as noted in the top banner. Leaving jobs queued will ensure that they are processed when this queue opens again. The simplest alternatives for temporary, resource intensive, high-priority work include cloud Galaxy instances and potentially Other public Galaxies. But you can also review all options on the Choices wiki, including a local Galaxy, which is very simple to get started with (5-15 minutes) and great for smaller tasks. http://wiki.galaxyproject.org/Cloud (Cloudman, etc.) http://wiki.galaxyproject.org/PublicGalaxyServers http://wiki.galaxyproject.org/BigPicture/Choices Please know that we are very much aware of the inconvinience this is causing our users. The upgrades to our underlying infrastructure are closer now, just a few weeks out. Thank you for your patience, Jen Galaxy team On 10/2/13 11:18 PM, Kumar Sankaran wrote: Hi all, I am trying to perform TopHat for Illumina from Galaxy's Main Server, and it is in queue for the past 3 to 4 days. Is this normal? Thanks Regards, Kumar. ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-user] Tophat Error: segment-based junction search failed with err
Hello, I don't know why I still have this problem.. I have run tophat2 with different dataset, sometimes it goes well but sometime I have this error. I run only one job at a time on a virtual machine with 8G memory without using galaxy plateform. I tried --no-coverage-search option but it changes nothing. Thanks. Delong De : Delong, Zhou Envoyé : 27 août 2013 9:36 À : galaxy-u...@bx.psu.edu Objet : Tophat Error: segment-based junction search failed with err Hello, I have run several analysis with Tophat 2 on my local instance of galaxy and I get this error for all of them.. segment-based junction search failed with err = 1 or -9 Here is an example of full error report: Error in tophat: [2013-08-23 11:56:58] Beginning TopHat run (v2.0.6) --- [2013-08-23 11:56:58] Checking for Bowtie Bowtie version:2.0.2.0 [2013-08-23 11:56:58] Checking for Samtools Samtools version:0.1.18.0 [2013-08-23 11:56:58] Checking for Bowtie index files [2013-08-23 11:56:58] Checking for reference FASTA file [2013-08-23 11:56:58] Generating SAM header for /usr/local/data/bowtie2/hg19/hg19 format: fastq quality scale: phred33 (default) [2013-08-23 11:58:04] Preparing reads left reads: min. length=50, max. length=50, 145339247 kept reads (34946 discarded) right reads: min. length=50, max. length=50, 145340153 kept reads (34040 discarded) [2013-08-23 14:16:21] Mapping left_kept_reads to genome hg19 with Bowtie2 [2013-08-24 01:04:37] Mapping left_kept_reads_seg1 to genome hg19 with Bowtie2 (1/2) [2013-08-24 03:38:22] Mapping left_kept_reads_seg2 to genome hg19 with Bowtie2 (2/2) [2013-08-24 05:29:58] Mapping right_kept_reads to genome hg19 with Bowtie2 [2013-08-24 19:50:22] Mapping right_kept_reads_seg1 to genome hg19 with Bowtie2 (1/2) [2013-08-24 22:36:38] Mapping right_kept_reads_seg2 to genome hg19 with Bowtie2 (2/2) [2013-08-25 01:40:37] Searching for junctions via segment mapping Coverage-search algorithm is turned on, making this step very slow Please try running TopHat again with the option (--no-coverage-search) if this step takes too much time or memory. [FAILED] Error: segment-based junction search failed with err =-9 Collecting potential splice sites in islands cp: cannot stat `/home/galaxy/galaxy-dist/database/job_working_directory/000/515/tophat_out/deletions.bed': No such file or directory cp: cannot stat `/home/galaxy/galaxy-dist/database/job_working_directory/000/515/tophat_out/insertions.bed': No such file or directory I did some research on the internet and it seems to be a memory problem to me, is there any solution other than rerun these jobs on a more powerful machine? And why has Bowtie/Tophat discard different numbers of reads? What will be the impact? Does it means that if I don't have exact matches between the paired end input, it is still be possible to run the job? Thanks, Delong ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] Tophat Error: segment-based junction search failed with err
Hi Delong, If you are mapping against a large reference genome and your datasets are large, 8G of memory may simply not be enough, even with omitting this paramater. Also, if you have set other TopHat parameters to be sensitive, then those can also be contributing to memory usage. Splitting the job up is still an option to try, as in the original post: http://gmod.827538.n3.nabble.com/Tophat-Error-segment-based-junction-search-failed-with-err-td4035978.html On 10/2/13 10:20 AM, Delong, Zhou wrote: Hello, I don't know why I still have this problem.. I have run tophat2 with different dataset, sometimes it goes well but sometime I have this error. There are likely content differences between the datasets. A tool such as FastQC is a good one to use to investigate. I run only one job at a time on a virtual machine with 8G memory without using galaxy plateform. I tried --no-coverage-search option but it changes nothing. Do you mean that the tool fails on the line command? Then it will also fail in Galaxy using the same resources, this is expected. If you do not want to split the job up, you could consider a Cloud Galaxy: http://usegalaxy.org/cloud Best, Jen Galaxy team Thanks. Delong *De :* Delong, Zhou *Envoyé :* 27 août 2013 9:36 *À :* galaxy-u...@bx.psu.edu *Objet :* Tophat Error: segment-based junction search failed with err Hello, I have run several analysis with Tophat 2 on my local instance of galaxy and I get this error for all of them.. segment-based junction search failed with err = 1 or -9 Here is an example of full error report: Error in tophat: [2013-08-23 11:56:58] Beginning TopHat run (v2.0.6) --- [2013-08-23 11:56:58] Checking for Bowtie Bowtie version:2.0.2.0 [2013-08-23 11:56:58] Checking for Samtools Samtools version:0.1.18.0 [2013-08-23 11:56:58] Checking for Bowtie index files [2013-08-23 11:56:58] Checking for reference FASTA file [2013-08-23 11:56:58] Generating SAM header for /usr/local/data/bowtie2/hg19/hg19 format: fastq quality scale: phred33 (default) [2013-08-23 11:58:04] Preparing reads left reads: min. length=50, max. length=50, 145339247 kept reads (34946 discarded) right reads: min. length=50, max. length=50, 145340153 kept reads (34040 discarded) [2013-08-23 14:16:21] Mapping left_kept_reads to genome hg19 with Bowtie2 [2013-08-24 01:04:37] Mapping left_kept_reads_seg1 to genome hg19 with Bowtie2 (1/2) [2013-08-24 03:38:22] Mapping left_kept_reads_seg2 to genome hg19 with Bowtie2 (2/2) [2013-08-24 05:29:58] Mapping right_kept_reads to genome hg19 with Bowtie2 [2013-08-24 19:50:22] Mapping right_kept_reads_seg1 to genome hg19 with Bowtie2 (1/2) [2013-08-24 22:36:38] Mapping right_kept_reads_seg2 to genome hg19 with Bowtie2 (2/2) [2013-08-25 01:40:37] Searching for junctions via segment mapping Coverage-search algorithm is turned on, making this step very slow Please try running TopHat again with the option (--no-coverage-search) if this step takes too much time or memory. [FAILED] Error: segment-based junction search failed with err =-9 Collecting potential splice sites in islands cp: cannot stat `/home/galaxy/galaxy-dist/database/job_working_directory/000/515/tophat_out/deletions.bed': No such file or directory cp: cannot stat `/home/galaxy/galaxy-dist/database/job_working_directory/000/515/tophat_out/insertions.bed': No such file or directory I did some research on the internet and it seems to be a memory problem to me, is there any solution other than rerun these jobs on a more powerful machine? And why has Bowtie/Tophat discard different numbers of reads? What will be the impact? Does it means that if I don't have exact matches between the paired end input, it is still be possible to run the job? Thanks, Delong ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of
Re: [galaxy-user] Tophat Error: segment-based junction search failed with err
Hi - Pls see below On 8/27/13 6:36 AM, Delong, Zhou wrote: Hello, I have run several analysis with Tophat 2 on my local instance of galaxy and I get this error for all of them.. segment-based junction search failed with err = 1 or -9 Here is an example of full error report: Error in tophat: [2013-08-23 11:56:58] Beginning TopHat run (v2.0.6) --- [2013-08-23 11:56:58] Checking for Bowtie Bowtie version:2.0.2.0 [2013-08-23 11:56:58] Checking for Samtools Samtools version:0.1.18.0 [2013-08-23 11:56:58] Checking for Bowtie index files [2013-08-23 11:56:58] Checking for reference FASTA file [2013-08-23 11:56:58] Generating SAM header for /usr/local/data/bowtie2/hg19/hg19 format: fastq quality scale: phred33 (default) [2013-08-23 11:58:04] Preparing reads left reads: min. length=50, max. length=50, 145339247 kept reads (34946 discarded) right reads: min. length=50, max. length=50, 145340153 kept reads (34040 discarded) [2013-08-23 14:16:21] Mapping left_kept_reads to genome hg19 with Bowtie2 [2013-08-24 01:04:37] Mapping left_kept_reads_seg1 to genome hg19 with Bowtie2 (1/2) [2013-08-24 03:38:22] Mapping left_kept_reads_seg2 to genome hg19 with Bowtie2 (2/2) [2013-08-24 05:29:58] Mapping right_kept_reads to genome hg19 with Bowtie2 [2013-08-24 19:50:22] Mapping right_kept_reads_seg1 to genome hg19 with Bowtie2 (1/2) [2013-08-24 22:36:38] Mapping right_kept_reads_seg2 to genome hg19 with Bowtie2 (2/2) [2013-08-25 01:40:37] Searching for junctions via segment mapping Coverage-search algorithm is turned on, making this step very slow Please try running TopHat again with the option (--no-coverage-search) if this step takes too much time or memory. [FAILED] Error: segment-based junction search failed with err =-9 Collecting potential splice sites in islands cp: cannot stat `/home/galaxy/galaxy-dist/database/job_working_directory/000/515/tophat_out/deletions.bed': No such file or directory cp: cannot stat `/home/galaxy/galaxy-dist/database/job_working_directory/000/515/tophat_out/insertions.bed': No such file or directory I did some research on the internet and it seems to be a memory problem to me, is there any solution other than rerun these jobs on a more powerful machine? Or modify the parameters, as suggested in the error report. You might also be able to run the job with smaller inputs by breaking them up into smaller datasets (paired), but how appropriate this is depends on what you plan to do with the mapped data after. And why has Bowtie/Tophat discard different numbers of reads? What will be the impact? Does it means that if I don't have exact matches between the paired end input, it is still be possible to run the job? Not having both ends of all pairs map in every experiment is probably expected. And you can certainly run the mapping job without even the initial FASTQ inputs having exactly the same set of matched pairs (for example: maybe some were filtered out differently during QA steps). The impact of having matched pairs will manifest in later steps in your analysis. And it depends on what you are doing how this needs to be manipulated upfront (or not!). Some tools, such as the Tuxedo RNA-seq tools, will filter down to matched pairs during later steps, such as Cufflinks, on their own. If doing variant calling, certain tools will also filter down to matched pairs or have tool form options to limit analysis to matched pairs - but others will expect that only matched pairs are input from the start. There are tools in the SAMTools tool group to filter/merge mapping results and tools in the Picard tool group to add/replace/merge labels or data results - all as needed. Each tool has help on the form itself, including links to the external source documentation. Hopefully this helps, Jen Galaxy team Thanks, Delong ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of
[galaxy-user] Tophat Error: segment-based junction search failed with err
Hello, I have run several analysis with Tophat 2 on my local instance of galaxy and I get this error for all of them.. segment-based junction search failed with err = 1 or -9 Here is an example of full error report: Error in tophat: [2013-08-23 11:56:58] Beginning TopHat run (v2.0.6) --- [2013-08-23 11:56:58] Checking for Bowtie Bowtie version:2.0.2.0 [2013-08-23 11:56:58] Checking for Samtools Samtools version:0.1.18.0 [2013-08-23 11:56:58] Checking for Bowtie index files [2013-08-23 11:56:58] Checking for reference FASTA file [2013-08-23 11:56:58] Generating SAM header for /usr/local/data/bowtie2/hg19/hg19 format: fastq quality scale: phred33 (default) [2013-08-23 11:58:04] Preparing reads left reads: min. length=50, max. length=50, 145339247 kept reads (34946 discarded) right reads: min. length=50, max. length=50, 145340153 kept reads (34040 discarded) [2013-08-23 14:16:21] Mapping left_kept_reads to genome hg19 with Bowtie2 [2013-08-24 01:04:37] Mapping left_kept_reads_seg1 to genome hg19 with Bowtie2 (1/2) [2013-08-24 03:38:22] Mapping left_kept_reads_seg2 to genome hg19 with Bowtie2 (2/2) [2013-08-24 05:29:58] Mapping right_kept_reads to genome hg19 with Bowtie2 [2013-08-24 19:50:22] Mapping right_kept_reads_seg1 to genome hg19 with Bowtie2 (1/2) [2013-08-24 22:36:38] Mapping right_kept_reads_seg2 to genome hg19 with Bowtie2 (2/2) [2013-08-25 01:40:37] Searching for junctions via segment mapping Coverage-search algorithm is turned on, making this step very slow Please try running TopHat again with the option (--no-coverage-search) if this step takes too much time or memory. [FAILED] Error: segment-based junction search failed with err =-9 Collecting potential splice sites in islands cp: cannot stat `/home/galaxy/galaxy-dist/database/job_working_directory/000/515/tophat_out/deletions.bed': No such file or directory cp: cannot stat `/home/galaxy/galaxy-dist/database/job_working_directory/000/515/tophat_out/insertions.bed': No such file or directory I did some research on the internet and it seems to be a memory problem to me, is there any solution other than rerun these jobs on a more powerful machine? And why has Bowtie/Tophat discard different numbers of reads? What will be the impact? Does it means that if I don't have exact matches between the paired end input, it is still be possible to run the job? Thanks, Delong ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] tophat to cuffdiff without cufflinks
Hello, You will need to provide a GTF or GFF3 file to Cuffdiff - this is what the tool uses as a reference base to build gene, transcript, and if provided in the annotation attributes, transcript start site and protein groupings to perform the differential analysis. More details can be found here: http://cufflinks.cbcb.umd.edu/manual.html Our tutorial and other wiki help is linked from here, see Tools on the Main Server: http://wiki.galaxyproject.org/Support#Interpreting_scientific_results Hopefully this helps, Jen Galaxy team On 5/30/13 3:15 PM, Colaneri, Alejandro Cesar wrote: Hi I comparing gen expression data (RNA-seq) in Arabidopsis. Different genotypes, different conditions. Since Arabidopsis is very well annotated I decided to do cuffdiff directly after tophat. However when building my workflow I found that the cuffdiff said a gtf file is necessary. Please see the picture in this email, under INPUT FORMAT. My question is if I can still compare my libraries in the way I designed below. // // ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] Tophat for Illumina is not running
Hello Lilach, The public Main Galaxy server is very busy right now, but I do see your account in the queue (as I have since you first sent this email). We expect the processing time to improve soon. Meanwhile, the best strategy is to leave queued job alone and not stop/restart or they will move back to the end of the queue. Or, if time is very urgent, consider a cloud version of Galaxy: http://usegalaxy.org/cloud Hopefully this helps to explain, Jen Galaxy team On 4/30/13 12:43 AM, lilach noy wrote: Hello, I'm new to Galaxy so I think i'm at the right place asking this, though please let me know if I got it all wrong. I sent a Tophat query on Thursday about 5 days ago and it is still waiting to ran (gray background). Is to O.k? A bug? Should i keep waiting or stop everything and restart? If this is not the address for reporting a suspicious bug, whom does this concern? Thank you very much, Lilach ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-user] Tophat for Illumina is not running
Hello, I'm new to Galaxy so I think i'm at the right place asking this, though please let me know if I got it all wrong. I sent a Tophat query on Thursday about 5 days ago and it is still waiting to ran (gray background). Is to O.k? A bug? Should i keep waiting or stop everything and restart? If this is not the address for reporting a suspicious bug, whom does this concern? Thank you very much, Lilach ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] tophat job help
Hello Dipanjana, I am not sure if you mean that the job is actually running (yellow) or has been waiting in the queue (grey) during this time period (or some combination), but I can let you know that both processes can vary in the length of time they take to execute. A job in the queue (grey) is waiting for its turn to run on the cluster. When Galaxy is busy, this time will be longer. For a job that is executing (yellow), it is important to know that not all jobs will complete in the same time period. Factors such as the number and content of query sequences, the size and content of the target genome, and run-time parameters all contribute to how long a job will run. I would expect that by now your job has completed and you know the outcome, and hopefully this helps to explain how the processing works. If time is urgent or a job exceeds the processing available on the public Main server, using Galaxy via the cloud is a good alternative: http://usegalaxy.org/cloud Best, Jen Galaxy team On 4/5/13 7:45 PM, Dipanjana Datta De wrote: Hi, I have been running a tophat job and it seems to run forever, its now 24 HRS . I do not understand, is it that i have done something wrong, the other tophat job took only 6 hrs. please help regards, Dipanjana -- /*Dipanjana Datta De*/ /*Postdoctoral Fellow*/ /*Department of Pharmacology and Toxicology*/ /*Virginia Commonwealth University*/ /*Richmond, Virginia*/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-user] Tophat mapping and Cufflinks output issues
Hello Galaxy Users- I've been using the Main Galaxy server to work on an RNA-Seq project for a non-model plant, and I've noticed that my output from Tophat and Cufflinks might not be as good as I'd like. I have a reference transcriptome assembled in Trinity, and it is based on the same Illumina-generated 100 bp reads I'm trying to map to it. When I use Tophat to map the reads to the reference transcriptome (I have trimmed the reads and filtered the lower quality ones), only about 10% of the reads actually map, so I go from 30,000,000 reads before mapping to 3,000,000 that are actually mapped. Therefore, I feel like I'm losing a lot of data. When I've changed the parameters to allow for more mismatches, not many more reads seem to map, and in many cases, the Tophat run fails and I receive the error message: *Settings: Output files: /tmp/ 3030460.cyberstar.psu.edu/tmpWbxTnm/dataset_5530451.*.ebwt Line rate: 6 (line is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 5 (one in 32) FTable chars: 10 Strings: unpacked Max bucket size: def*. I've had similar numbers of reads map with Bowtie by itself and BWA as well. I've also tried mapping the reads to the assembled isoforms (contigs) of the transcriptome, and this results in many more reads (close to 90%) being mapped. Therefore, I figure the reads should map to the reference transcriptome, and I'm not sure why this isn't happening. The other issue I've run into is that in Cuffdiff only about 4,800 genes appear in the output files as being tested for differential expression. There are approximately 100,000 genes in the reference transcriptome, so I was thinking that there should be more than ca. 4,800 that are tested for differential expression. Should each gene be tested? Does Cuffdiff just not report some of the genes that are not differentially expressed, or is the program not testing all of the genes? If anyone can provide some help, guidance, or a suggestion, I'd greatly appreciate it. Thanks, and take care. Jim ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Tophat error.
Hello Humberto, Are you using the public Main Galaxy instance at http://main.g2.bx.psu.edu (http://usegalaxy.org)? If so, and a re-run of the job still fails, please submit a bug report so that we can provide feedback. http://wiki.galaxyproject.org/Support#Reporting_tool_errors There was a small issue with reporting bugs the last few days that has since been resolved, so if you tried this earlier, and it failed, please try again now. Best, Jen Galaxy team On 12/9/12 9:30 AM, Humberto Boncristiani wrote: Hi Everyone. Somebody knows what this error message means: An error occurred running this job:/Settings: Output files: /tmp/3010855.cyberstar.psu.edu/tmpU4RslD/tmpNmgc_h.*.ebwt Line rate: 6 (line is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 5 (one in 32) FTable chars: 10 Strings: unpacked Max bucket size: default/ / / /Thanks./ / / *Humberto. * ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] Tophat error.
Hi Everyone. Somebody knows what this error message means: An error occurred running this job:Settings: Output files: /tmp/3010855.cyberstar.psu.edu/tmpU4RslD/tmpNmgc_h.*.ebwt Line rate: 6 (line is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 5 (one in 32) FTable chars: 10 Strings: unpacked Max bucket size: default Thanks. Humberto. ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] Tophat alignment statistics?
Hi, galaxy users How to get Tophat alignment statistics such as % of reads aligned to exon, intron, splice junction? is there a Log file available? How many unique and mutiple alignments? I use Bam index, Flagstat, and Bam alignment metrix in Galaxy, but none reported the information I need. -- Wei Liao Research Scientist, Brentwood Biomedical Research Institute 16111 Plummer St. Bldg 7, Rm D-122 North Hills, CA 91343 818-891-7711 ext 7645 ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Tophat alignment statistics?
Hi Wei, Have a look at RNASeQC which provides more than what you specified here. (https://confluence.broadinstitute.org/display/CGATools/RNA-SeQC) This generates a detailed report with all relevant metrics on your RNA data.. I think, integrating this - a java based tool - into Galaxy should resolve your problem. Hope this helps. Raj From: galaxy-user-boun...@lists.bx.psu.edu [mailto:galaxy-user-boun...@lists.bx.psu.edu] On Behalf Of Wei Liao Sent: Friday, December 07, 2012 3:57 AM To: galaxy-user@lists.bx.psu.edu Subject: [galaxy-user] Tophat alignment statistics? Hi, galaxy users How to get Tophat alignment statistics such as % of reads aligned to exon, intron, splice junction? is there a Log file available? How many unique and mutiple alignments? I use Bam index, Flagstat, and Bam alignment metrix in Galaxy, but none reported the information I need. -- Wei Liao Research Scientist, Brentwood Biomedical Research Institute 16111 Plummer St. Bldg 7, Rm D-122 North Hills, CA 91343 818-891-7711 ext 7645 This e-mail contains PRIVILEGED AND CONFIDENTIAL INFORMATION intended solely for the use of the addressee(s). If you are not the intended recipient, please notify the sender by e-mail and delete the original message. Further, you are not to copy, disclose, or distribute this e-mail or its contents to any other person and any such actions that are unlawful. This e-mail may contain viruses. Ocimum Biosolutions has taken every reasonable precaution to minimize this risk, but is not liable for any damage you may sustain as a result of any virus in this e-mail. You should carry out your own virus checks before opening the e-mail or attachment. The information contained in this email and any attachments is confidential and may be subject to copyright or other intellectual property protection. If you are not the intended recipient, you are not authorized to use or disclose this information, and we request that you notify us by reply mail or telephone and delete the original message from your mail system. OCIMUMBIO SOLUTIONS (P) LTD___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] tophat
It isn't normal, but this can happen during periods of extremely high load like we're currently experiencing. If you leave your jobs in the queue, they'll execute as soon as possible - don't cancel or restart your jobs as this will only move them to the back of the queue and delay completion. -Dannon On Nov 8, 2012, at 5:13 AM, Vevis, Christis christis.vevis...@ucl.ac.uk wrote: Hi all, I am trying to perform tophat for illumina from the main server of galaxy and is in queue for 24 hours…is that normal?? Regards Kristis Vevis, PhD Student Cell Biology UCL Institute of Ophthalmology 11-43 Bath Street London EC1V 9EL, UK 020 7608 4067 ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] Tophat results
Dear galaxy users, I aligned my RNA-seq data by using Tophat in galaxy. It generated some Tophat deletions, Tophat insertions and Tophat splice junctions results. These are all BED files. Does anyone know how to use/analyze these kind of results? Also, I used illumina RNA-seq. Each biological sample has 36-48 million reads. The data for each sample were divided to 10-12 FASTQ files. When I did the FASTQ Summary Statistics and draw boxplot for each of the sub-file, the score value is about 9-10. Is it too low? Shall I combine the FASTQ files for each biological sample and do the statistics again? At last, does anyone know how to convert a long list of zebrafish genes (500-1000 genes) to human or mammalian orthologs? Thank you for your replies, Xiefan Fang University of Florida ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] Tophat settings
Dear All, I am not so sure about two Tophat settings. Please help. 1) Number of mismatches allowed in the initial read mapping Based on the documantation, my understanding is: the reads are re-aligned to transcriptome/genome if the mismatches in the initial alignment is more than the set number (for example, the default setting is 2). In other words, the re-aligning will continue until the mismatches is equal to or below the set number. Is my understanding correct? If I am right, I have one worry: will Tophat stop re-aligning if the mismatch is below 2 (if I use the default setting). If it is true, the read will not be aligned to where it belongs to (with 0 mismatch). 2) Number of mismatches allowed in each segment alignment for reads mapped independently Does this mean that the reads will be cut into segments if the mismatches of alignment is more than the set number? Thanks in advance. Jianguang ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] tophat deletions output
Hello Irene, The file is described in the TopHat manual: http://tophat.cbcb.umd.edu/manual.html#output Along with the insertion files, deletions describes variation between the query and the reference genome at the base level (nucleotide). It does not describe whole transcripts or genes. How to use this information is really up to you. This is very large and popular topic area with more information then I could outline in a simple email reply. Even in Galaxy there are many tools and data sources complete with descriptions and help and links to even more resources. More of these are under active development. The base way to start is with some research: Galaxy searches in the Tool panel, Pages, Workflows, Tool Shed, the Wiki, Galaxy custom google searches or even just a plain Google with keywords like SNP or Variation or Indel or similar, alone or in combination, should get you going, if this interests you. Take care, Jen Galaxy team On 8/21/12 4:27 AM, i b wrote: dear all, how can we use the tophat deletions output? e.g. if I want to see and conpare between two samples if a specific gene or transcript had been deleted, how can I use this output? is visualisation enough? thanks, ib ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] tophat deletions output
dear all, how can we use the tophat deletions output? e.g. if I want to see and conpare between two samples if a specific gene or transcript had been deleted, how can I use this output? is visualisation enough? thanks, ib ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] tophat output spice junction output
Hello Irene, Please see: http://wiki.g2.bx.psu.edu/Learn/Datatypes#Learn.2BAC8-Datatypes.Bed The BED data format was created by UCSC: http://genome.ucsc.edu/FAQ/FAQformat.html#format1 The TopHat manual also links to the UCSC specification: http://tophat.cbcb.umd.edu/manual.html (scroll to TopHat Output) Thanks! Jen Galaxy team On 7/20/12 5:34 AM, i b wrote: Hi, where can I find an explanation of the columns in the splice junctions output? From 7 to12 they are only numbered thanks, ib ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] tophat output spice junction output
Hi, where can I find an explanation of the columns in the splice junctions output? From 7 to12 they are only numbered thanks, ib ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] Tophat
Hello, Using the defaults and then testing the resulting SAM output seems to be what most folks are doing if they do not have access to the original library construction methods (e.g. size selection). Both SAM Tools and Picard are in Galaxy. This is a useful post where the options are discussed: http://www.biostars.org/post/show/16556/estimate-insert-size-in-paired-endmate-pair/ Is the data Illumina? The data source may be able to tell you if the adapter sequence was actually sequenced and/or if it was removed already or not. If present or you just suspect it is present, they would also have access to the Illumina fasta adapter data. You could also test with FastQC (before or after alignment, maybe on just a sample), then perform a clip based on those results, and re-run. See the tools in 'NGS: QC and manipulation' to perform these tasks. Going forward, please send questions as a new thread directly to our mailing list at galaxy-u...@bx.psu.edu. http://wiki.g2.bx.psu.edu/Support#Public_mailing_list_Q_.26_A_discussions Best, Jen Galaxy team On 7/10/12 5:36 AM, asma.bioi...@gmail.com wrote: Does anyone got correct answer, how to extract the correct distance between two pairs? One naive question, how can I find the adapter sequence length? Thanks! -- Jennifer Jackson http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] Tophat and Bowtie2
Hi, I installed bowtie2 and when running tophat I get the following error: Error in tophat: [2012-06-19 14:02:39] Beginning TopHat run (v2.0.3) --- [2012-06-19 14:02:39] Checking for Bowtie Bowtie version:2.0.0.6 [2012-06-19 14:02:39] Checking for Samtools Samtools version:0.1.18.0 [2012-06-19 14:02:39] Checking for Bowtie index files Error: Could not find Bowtie 2 index files (/tmp/tmpojo7bV/AgamP3.14.dna.toplevel.*.bt2) I was wondering if I can create the index files using bowtie2 via command line and then change the universe_wsgi.ini to: # Temporary files are stored in this directory. new_file_path = database/tmp and put the index files there. Anyway, why is it not creating the indexes? I created links to all bowtie2 executable files. If I remove bowtie 0.12.8, then I get a error from tophat (bowtie not installed). Is it creating the index with bowtie 0.12.8? Thank you. Luciano ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Tophat and Bowtie2
Hi, I actually fixed it. I changed the wrapper in the line 105 from: cmd_index = 'bowtie-build %s -f %s %s' % ( space, options.own_file, index_path ) to cmd_index = 'bowtie2-build %s -f %s %s' % ( space, options.own_file, index_path ) Luciano On Tue, Jun 19, 2012 at 3:03 PM, Luciano Cosme cosme.sim...@gmail.comwrote: Hi, I installed bowtie2 and when running tophat I get the following error: Error in tophat: [2012-06-19 14:02:39] Beginning TopHat run (v2.0.3) --- [2012-06-19 14:02:39] Checking for Bowtie Bowtie version:2.0.0.6 [2012-06-19 14:02:39] Checking for Samtools Samtools version:0.1.18.0 [2012-06-19 14:02:39] Checking for Bowtie index files Error: Could not find Bowtie 2 index files (/tmp/tmpojo7bV/AgamP3.14.dna.toplevel.*.bt2) I was wondering if I can create the index files using bowtie2 via command line and then change the universe_wsgi.ini to: # Temporary files are stored in this directory. new_file_path = database/tmp and put the index files there. Anyway, why is it not creating the indexes? I created links to all bowtie2 executable files. If I remove bowtie 0.12.8, then I get a error from tophat (bowtie not installed). Is it creating the index with bowtie 0.12.8? Thank you. Luciano -- *Luciano Cosme* - PhD Candidate Texas AM Entomology Vector Biology Research Group www.lcosme.com 979 845 1885 co...@tamu.edu - ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Tophat mapping
I am wondering if these non-coding reads will be included when cufflinks calculates transcript/gene expression. Reads will only be included if they map to assembled/known transcripts. And another question is: how to know the number of reads mapped to a certain exon? This isn't possible because a single read may map to multiple exons and/or transcripts. Cufflinks assigns reads probabilistically when their mapping cannot be uniquely determined. See http://cufflinks.cbcb.umd.edu/faq.html#count http://cufflinks.cbcb.umd.edu/howitworks.html for details. Best, J.___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Tophat mapping
Jeremy, do you have a workflow to estimate what percent of the reads are mapping to unknown expressed regions? Here's a simple approach assuming mapped reads are in BAM format: BAM -- SAM SAM -- Interval Intersect reads as interval with known annotation not allowing for any overlap. Best, J. ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Tophat paired end read
Hello Jiwen, No, you do not need to join the files for the quality processing. Hopefully this helps! Best, Jen Galaxy team On 4/9/12 9:14 AM, 杨继文 wrote: Hi all, I have paired end RNA-Seq reads ( Illumina Hiseq 2000) in seperate files. Before mapping, I need to trim the reads. My questions is : Do I have to join pair end reads before timming, and then split again for Tophat??? Lookiong forward to your answers. Thanks Jiwen ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Tophat paired end read
Jiwen, I wonder if you are thinking about the situation where you could be discarding reads that are to short after trimming?. In that case you could be getting the two files out of sync. If this is the case, I think you do need to join the files first, do the trimming and then take them apart again. Regards, Carlos On Mon, Apr 9, 2012 at 1:25 PM, Jennifer Jackson j...@bx.psu.edu wrote: Hello Jiwen, No, you do not need to join the files for the quality processing. Hopefully this helps! Best, Jen Galaxy team On 4/9/12 9:14 AM, 杨继文 wrote: Hi all, I have paired end RNA-Seq reads ( Illumina Hiseq 2000) in seperate files. Before mapping, I need to trim the reads. My questions is : Do I have to join pair end reads before timming, and then split again for Tophat??? Lookiong forward to your answers. Thanks Jiwen ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] Tophat error
Hi, JUst running a TopHat job which returned the following error: Executing: /gpfs/cluster/isys/galaxy/Software/bin/bowtie-inspect /local/tmp5Ywx45/dataset_942 ./tophat_out/tmp/dataset_942.fa [Tue Mar 13 12:45:08 2012] Checking for Bowtie Bowtie version: 0.12.7.0 [Tue Mar 13 12:45:08 2012] Checking for Samtools Samtools Version: 0.1.18 [Tue Mar 13 12:45:08 2012] Generating SAM header for /local/tmp5Ywx45/dataset_942 format: fastq quality scale: phred33 (default) [Tue Mar 13 12:45:21 2012] Preparing reads left reads: min. length=56, count=29523921 right reads: min. length=56, count=29543412 [Tue Mar 13 13:07:54 2012] Mapping left_kept_reads against dataset_942 with Bowtie [Tue Mar 13 13:45:26 2012] Processing bowtie hits [Tue Mar 13 14:11:28 2012] Mapping left_kept_reads_seg1 against dataset_942 with Bowtie (1/2) [Tue Mar 13 14:43:27 2012] Mapping left_kept_reads_seg2 against dataset_942 with Bowtie (2/2) [Tue Mar 13 14:57:50 2012] Mapping right_kept_reads against dataset_942 with Bowtie [Tue Mar 13 15:37:46 2012] Processing bowtie hits [Tue Mar 13 16:04:28 2012] Mapping right_kept_reads_seg1 against dataset_942 with Bowtie (1/2) [Tue Mar 13 16:37:18 2012] Mapping right_kept_reads_seg2 against dataset_942 with Bowtie (2/2) [Tue Mar 13 16:50:40 2012] Searching for junctions via segment mapping Traceback (most recent call last): File /gpfs/cluster/isys/galaxy/Software/bin/tophat, line 3063, in module sys.exit(main()) File /gpfs/cluster/isys/galaxy/Software/bin/tophat, line 3029, in main user_supplied_deletions) File /gpfs/cluster/isys/galaxy/Software/bin/tophat, line 2681, in spliced_alignment [maps[initial_reads[left_reads]].unspliced_bwt, maps[initial_reads[left_reads]].seg_maps[-1]], TypeError: list indices must be integers, not str Does anyone know what this kind of error is? Best Wishes, David. __ Dr David A. Matthews Senior Lecturer in Virology Room E49 Department of Cellular and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol Bristol. BS8 1TD U.K. Tel. +44 117 3312058 Fax. +44 117 3312091 d.a.matth...@bristol.ac.uk ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] Tophat error
Hi, JUst running a TopHat job which returned the following error: Executing: /gpfs/cluster/isys/galaxy/Software/bin/bowtie-inspect /local/tmp5Ywx45/dataset_942 ./tophat_out/tmp/dataset_942.fa [Tue Mar 13 12:45:08 2012] Checking for Bowtie Bowtie version: 0.12.7.0 [Tue Mar 13 12:45:08 2012] Checking for Samtools Samtools Version: 0.1.18 [Tue Mar 13 12:45:08 2012] Generating SAM header for /local/tmp5Ywx45/dataset_942 format: fastq quality scale: phred33 (default) [Tue Mar 13 12:45:21 2012] Preparing reads left reads: min. length=56, count=29523921 right reads: min. length=56, count=29543412 [Tue Mar 13 13:07:54 2012] Mapping left_kept_reads against dataset_942 with Bowtie [Tue Mar 13 13:45:26 2012] Processing bowtie hits [Tue Mar 13 14:11:28 2012] Mapping left_kept_reads_seg1 against dataset_942 with Bowtie (1/2) [Tue Mar 13 14:43:27 2012] Mapping left_kept_reads_seg2 against dataset_942 with Bowtie (2/2) [Tue Mar 13 14:57:50 2012] Mapping right_kept_reads against dataset_942 with Bowtie [Tue Mar 13 15:37:46 2012] Processing bowtie hits [Tue Mar 13 16:04:28 2012] Mapping right_kept_reads_seg1 against dataset_942 with Bowtie (1/2) [Tue Mar 13 16:37:18 2012] Mapping right_kept_reads_seg2 against dataset_942 with Bowtie (2/2) [Tue Mar 13 16:50:40 2012] Searching for junctions via segment mapping Traceback (most recent call last): File /gpfs/cluster/isys/galaxy/Software/bin/tophat, line 3063, in module sys.exit(main()) File /gpfs/cluster/isys/galaxy/Software/bin/tophat, line 3029, in main user_supplied_deletions) File /gpfs/cluster/isys/galaxy/Software/bin/tophat, line 2681, in spliced_alignment [maps[initial_reads[left_reads]].unspliced_bwt, maps[initial_reads[left_reads]].seg_maps[-1]], TypeError: list indices must be integers, not str Does anyone know what this kind of error is? Best Wishes, David. __ Dr David A. Matthews Senior Lecturer in Virology Room E49 Department of Cellular and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol Bristol. BS8 1TD U.K. Tel. +44 117 3312058 Fax. +44 117 3312091 d.a.matth...@bristol.ac.uk ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Tophat error
Hi David, You question has posted to the list now and we will be getting back to you. It didn't post immediately due to some mail mailman server issues here. This looks like a problem that came up on a local instance. Because of that, I am going to send this over to the galaxy-...@bx.psu.edu mailing list. At first glance, this appears to be a problem with the NGS genome indexes used for the target genome. These are the instructions you followed? http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup (Bowtie indexes are used for TopHat) We will be looking at this more later today, but I wanted to get back to you, so you that you know that this doesn't need to be posted again. Thanks! Jen Galaxy team On 3/14/12 6:48 AM, David Matthews wrote: Hi, JUst running a TopHat job which returned the following error: Executing: /gpfs/cluster/isys/galaxy/Software/bin/bowtie-inspect /local/tmp5Ywx45/dataset_942 ./tophat_out/tmp/dataset_942.fa [Tue Mar 13 12:45:08 2012] Checking for Bowtie Bowtie version: 0.12.7.0 [Tue Mar 13 12:45:08 2012] Checking for Samtools Samtools Version: 0.1.18 [Tue Mar 13 12:45:08 2012] Generating SAM header for /local/tmp5Ywx45/dataset_942 format: fastq quality scale: phred33 (default) [Tue Mar 13 12:45:21 2012] Preparing reads left reads: min. length=56, count=29523921 right reads: min. length=56, count=29543412 [Tue Mar 13 13:07:54 2012] Mapping left_kept_reads against dataset_942 with Bowtie [Tue Mar 13 13:45:26 2012] Processing bowtie hits [Tue Mar 13 14:11:28 2012] Mapping left_kept_reads_seg1 against dataset_942 with Bowtie (1/2) [Tue Mar 13 14:43:27 2012] Mapping left_kept_reads_seg2 against dataset_942 with Bowtie (2/2) [Tue Mar 13 14:57:50 2012] Mapping right_kept_reads against dataset_942 with Bowtie [Tue Mar 13 15:37:46 2012] Processing bowtie hits [Tue Mar 13 16:04:28 2012] Mapping right_kept_reads_seg1 against dataset_942 with Bowtie (1/2) [Tue Mar 13 16:37:18 2012] Mapping right_kept_reads_seg2 against dataset_942 with Bowtie (2/2) [Tue Mar 13 16:50:40 2012] Searching for junctions via segment mapping Traceback (most recent call last): File /gpfs/cluster/isys/galaxy/Software/bin/tophat, line 3063, inmodule sys.exit(main()) File /gpfs/cluster/isys/galaxy/Software/bin/tophat, line 3029, in main user_supplied_deletions) File /gpfs/cluster/isys/galaxy/Software/bin/tophat, line 2681, in spliced_alignment [maps[initial_reads[left_reads]].unspliced_bwt, maps[initial_reads[left_reads]].seg_maps[-1]], TypeError: list indices must be integers, not str Does anyone know what this kind of error is? Best Wishes, David. __ Dr David A. Matthews Senior Lecturer in Virology Room E49 Department of Cellular and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol Bristol. BS8 1TD U.K. Tel. +44 117 3312058 Fax. +44 117 3312091 d.a.matth...@bristol.ac.uk mailto:d.a.matth...@bristol.ac.uk ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Tophat Mean Inner Distance between Mate Pairs
Hi JIwen, As the seqanswers thread shows, there is some debate about this. One of the last posts there makes the most sense - where fragment length is defined as the total genome bases covered by the aligned paired sequences: tip of 5' start, through the gap, to the very 3' tail end and where mean inner distance is the gap in the middle (between the paired seqs) where there is no alignment. This could be tested with smaller samples of data and compared to your fragment selection, to see how it matches up. But, for a definitive answer, asking the tool authors is the best bet. The contact information is: tophat.cuffli...@gmail.com If you are given a reply that explains the calculation, it would be great if the TopHat documentation itself were updated. http://tophat.cbcb.umd.edu/manual.html And we would be very glad to hear of the details, so that here at Galaxy we could add the information to our RNA-seq help and the searchable mailing list archives. Great question! If we find out ourselves meanwhile, an update will be posted back here to the mailing list, Best, Jen Galaxy team On 3/6/12 12:23 PM, 杨继文 wrote: Hi all, When mapping pair end RNA-seq reads using tophat, we need to type in Mean Inner Distance between Mate Pairs. In galaxy, we can read the following information: This is the expected (mean) inner distance between mate pairs. For, example, for paired end runs with fragments selected at 300bp, where each end is 50bp, you should set -r to be 200. There is no default, and this parameter is required for paired end runs. I think the size of fragment (here 300bp) includes not only the length of pair end reads, but also the length of adaptors. so, maybe the Mean Inner Distance between Mate Pairs should be : fragment length - pair end read length - adaptor length. Am I right? or did I miss something? Is it a must to type in the accurate value? Looking forward to your reply JIwen ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Tophat
Hello Jiwen, The tool NGS: Picard (beta) - SAM/BAM Alignment Summary Metrics gives a nice set of statistics for paired end data. Hopefully this helps, Best, Jen Galaxy team On 3/7/12 12:35 AM, 杨继文 wrote: Dear all, This might be a silly question, but I couldn't figure it out by myself :-((. Could you please tell me how I can find out how many reads have been mapped to the genome after running Tophat for pair end RNA seq data? Thanks in advance. JIwen ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] Tophat
Dear all, This might be a silly question, but I couldn't figure it out by myself :-((. Could you please tell me how I can find out how many reads have been mapped to the genome after running Tophat for pair end RNA seq data? Thanks in advance. JIwen___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] Tophat Mean Inner Distance between Mate Pairs
Hi all, When mapping pair end RNA-seq reads using tophat, we need to type in Mean Inner Distance between Mate Pairs. In galaxy, we can read the following information: This is the expected (mean) inner distance between mate pairs. For, example, for paired end runs with fragments selected at 300bp, where each end is 50bp, you should set -r to be 200. There is no default, and this parameter is required for paired end runs. I think the size of fragment (here 300bp) includes not only the length of pair end reads, but also the length of adaptors. so, maybe the Mean Inner Distance between Mate Pairs should be : fragment length - pair end read length - adaptor length. Am I right? or did I miss something? Is it a must to type in the accurate value? Looking forward to your reply JIwen ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Tophat Mean Inner Distance between Mate Pairs
Hi Jiwen, This is a subject that has me very confused too. This thread at seqanswer didn't help much either: http://seqanswers.com/forums/showthread.php?t=8730 But it does have some good comments on the subject. I did try using the two possible options I can think of: fragment length - pair end read length - adaptor length And: fragment length - pair end read length With the latter I get around 10% increase on properly paired reads. I wonder if Tophat internally takes into account the adapters. Still, it would be nice to get a definitive answer in this subject. Regards, Carlos 2012/3/6 杨继文 jiwenyang0...@126.com: Hi all, When mapping pair end RNA-seq reads using tophat, we need to type in Mean Inner Distance between Mate Pairs. In galaxy, we can read the following information: This is the expected (mean) inner distance between mate pairs. For, example, for paired end runs with fragments selected at 300bp, where each end is 50bp, you should set -r to be 200. There is no default, and this parameter is required for paired end runs. I think the size of fragment (here 300bp) includes not only the length of pair end reads, but also the length of adaptors. so, maybe the Mean Inner Distance between Mate Pairs should be : fragment length - pair end read length - adaptor length. Am I right? or did I miss something? Is it a must to type in the accurate value? Looking forward to your reply JIwen ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] TopHat version in GALAXY
Dear all: I have GALAXY installed in a UNIX server. BOWTIE works fine but TOPHAT and CUFFDIFF crash upon starting. In the case of TOPHAT, I noticed that GALAXY has a 1.5.0 version integrated, while the TOPHAT website claims the latest version is 1.4.1. My question is which are the best/appropiate TOPHAT and CUFFDIFF versions? The error message I get is TOPHAT not recognized. Any other suggestions? Thanks, G. ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] Tophat settings
In the new version of tophat they allow for over 3 mismatches in the initial alignment, however your server still gives an error if you attempt to move this over 3. This is problematic for trying to map RNAseq reads where there is moderate divergence between the RNA and the reference genome. Jack ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] Tophat
Dear all, Today I used Tophat to map the reads from RNA-Seq, and had a look at the results using visaulization function. In some regions I can see splice junctions calculated by Tophat, but I don't see any reads mapping to this region. Is this a bit strange? I thought splice junction is calculated from the mapped reads. However, I think cufflinks only uses accepted hits as input, maybe it is not a big problem that splice junction' is not accurate. Am I right? Was there something wrong when I mapped my reads with tophat? Hope you can help me figure it out. Looking forward to hearing from you. Jiwen ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Tophat
Hello Jiwen, It is possible to view both the TopHat and Cufflinks output together in Trackster. Are you doing this? Are you seeing that reads/transcripts are spanning the splice regions (align to one side, span the gap, then align to the other side)? This is what would be expected for RNA-seq data. It might help to import a known transcript track from UCSC or Biomart and visualize that, to get a better understanding of how genomic features are represented in the Trackster UI. If you have an error dataset from an RNA-seq tool, you can send in a bug report, but that doesn't seem to be the case. Rather, there is a question about how the calculation are done. For cases like that, the tool authors might be the best source for help. Contact info is in this wiki link Example: unexpected results with RNA-seq analysis tools. http://wiki.g2.bx.psu.edu/Support#Unexpected_scientific_result Hopefully this helps, Best, Jen Galaxy team On 2/3/12 7:24 AM, 杨继文 wrote: Dear all, Today I used Tophat to map the reads from RNA-Seq, and had a look at the results using visaulization function. In some regions I can see splice junctions calculated by Tophat, but I don't see any reads mapping to this region. Is this a bit strange? I thought splice junction is calculated from the mapped reads. However, I think cufflinks only uses accepted hits as input, maybe it is not a big problem that splice junction' is not accurate. Am I right? Was there something wrong when I mapped my reads with tophat? Hope you can help me figure it out. Looking forward to hearing from you. Jiwen ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Tophat jobs not starting
On Dec 14, 2011, at 11:19 AM, Magdalena Strzelecka wrote: Hi, I have submitted some jobs to Tophat, but they have not started since yesterday (Dec 13th); i.e they were in a queue for 12 hrs. I have re-submitted everything again (2 jobs), but the same situation is happening. Is there some issue with Tophat at the moment? Hi Magdalena, This was due to a problem with the cluster Galaxy uses to run certain jobs. This was resolved early last week, although there may have been a few intermittent problems after that time. If tophat still has not run successfully, please let us know. Our sincere apologies for the inconvenience, Best, --nate Thanks. M. -- Magdalena Strzelecka, PhD Heald Lab University of California, Berkeley Department of Molecular Cell Biology 315 Life Sciences Addition # 3200 Berkeley, CA 94720-3200 phone: (510) 643-5002 fax: (510) 643-6791 e-mail: strzele...@berkeley.edu ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] Tophat jobs not starting
Hi, I have submitted some jobs to Tophat, but they have not started since yesterday (Dec 13th); i.e they were in a queue for 12 hrs. I have re- submitted everything again (2 jobs), but the same situation is happening. Is there some issue with Tophat at the moment? Thanks. M. -- Magdalena Strzelecka, PhD Heald Lab University of California, Berkeley Department of Molecular Cell Biology 315 Life Sciences Addition # 3200 Berkeley, CA 94720-3200 phone: (510) 643-5002 fax: (510) 643-6791 e-mail: strzele...@berkeley.edu ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] TopHat
Hello Tao, The tools in the group NGS: Picard (beta) - QC/Metrics for sam/bam can generate statistics, in particular the tool SAM/BAM Alignment Summary Metrics. Another choice is NGS: SAM Tools - flagstat. If more statistics are needed, then starting with the original FASTQ and the mapping result SAM file, the tools in Text Manipulation, Filter and Sort, and Join, and Subtract and Group can be used in custom combinations. This question was almost missed. I was able to locate, format, and send as a new thread to the appropriate mailing list. Hopefully this reply helps or you have already found the tools above. Please help us to track new questions and provide prompt help by sending tool and data questions: 1 - to either galaxy-u...@bx.psu.edu or galaxy-...@bx.psu.edu, which are best for most questions. sending to galaxy-b...@bx.psu.edu is mainly reserved for UI bug reports (green bug icon for failed datasets) or for sending shared links to private data. http://wiki.g2.bx.psu.edu/Support#Public_mailing_list_Q_.26_A_discussions 2 - with the to as the mailing list address galaxy-u...@bx.psu.edu. When a brand new question is sent with the mailing list as a cc, it is not tracked. 3 - when a new question is sent as a reply to an earlier thread with a new subject line, it is not tracked. start a new thread for new questions with new subject lines. 4 - please use reply-all if you would like more assistance about the same subject to keep the thread consistent for the user community. Thank you for your help with this! Best, Jen Galaxy team Peng, Tao wrote: Hi jen, after I did TopHat analysis of groomed FASTAQ data, how can I find information on how many total reads went into TopHat? How many reads were removed? How many unique hits to reference genome? I was trying to prepare a table for presentation and realize that I could NOT find the information in my GALAXY account? Thanks, tao -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] TopHat/Cufflinks visualization
How do people on this mailing list usually visualize Tophat and/or Cufflinks results (eg. tracks on UCSC browser)? I have only this once before, and I started with a .wig file that I uploaded to the genome browser, however it looks like Tophat does not give any .wig file in the output. Suggestions? Thanks! A ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] TopHat/Cufflinks visualization
Hi Alessia, Shamsher is correct, Trackster is a great choice for viewing data. The Galaxy Track Browser (aka Trackster) has several new features and more coming up in the next few weeks at the Main instance. This tutorial covers a basic RNA-seq analysis that includes visualization: http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise And this wiki explains the details. One brand new feature (undocumented) allows a custom genome to be used in fasta format from your history (same basic instructions as in the wiki for a custom genome browser creation, but use the fasta file instead of a .len file). So whether your genome is native to Galaxy, or UCSC, or not, Trackster can display multiple tracks at full chromosome or zoomed view with user-defined display options: http://wiki.g2.bx.psu.edu/Learn/Visualization Hopefully this will work out for you! Best, Jen Galaxy team On 11/9/11 9:37 AM, Alessia D wrote: How do people on this mailing list usually visualize Tophat and/or Cufflinks results (eg. tracks on UCSC browser)? I have only this once before, and I started with a .wig file that I uploaded to the genome browser, however it looks like Tophat does not give any .wig file in the output. Suggestions? Thanks! A ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] tophat error
Hello, I was trying to run tophat v1.3.2 on SOLID data and I have this error: zohra@bart:~/Bureau/cancer$ tophat -o /tmp/tophat_SRR036752/ -g 1 -p 4 -C /home/zohra/indexes_bowtie/humain_ SRR036752.fastq [Tue Oct 11 13:23:53 2011] Beginning TopHat run (v1.3.2) --- [Tue Oct 11 13:23:53 2011] Preparing output location /tmp/tophat_SRR036752// [Tue Oct 11 13:23:53 2011] Checking for Bowtie index files [Tue Oct 11 13:23:53 2011] Checking for reference FASTA file [Tue Oct 11 13:23:53 2011] Checking for Bowtie Bowtie version: 0.12.7.0 [Tue Oct 11 13:23:53 2011] Checking for Samtools Samtools Version: 0.1.18 [Tue Oct 11 13:23:53 2011] Generating SAM header for /home/zohra/indexes_bowtie/humain_ [Tue Oct 11 13:23:55 2011] Preparing reads format: fastq quality scale: phred33 (default) [FAILED] Error running 'prep_reads' Error: qual length (51) differs from seq length (51) for fastq record ! Can you help me. Thanks Zohra Saci ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] tophat error
Hello Zohra, For command line (not Galaxy) use of this tool, questions would be best directed to the tool authors at tophat.cuffli...@gmail.com. That said, there appears to be a mismatch between the quality scores in your fastq file and what was expected (integer, linked to the -C option). Should you decide to use Galaxy at http://usegalaxy.org, there are tools to format the input and run this type of job. To help you get started, please see our tutorial covering this exact type of analysis: http://wiki.g2.bx.psu.edu/Learn/Screencasts see Examples of other analyses - SOLiD Single End Hopefully one of these options will work out for you, Best, Jen Galaxy team On 10/11/11 7:47 AM, zohra saci wrote: Hello, I was trying to run tophat v1.3.2 on SOLID data and I have this error: *zohra@bart:~/Bureau/cancer$ tophat -o /tmp/tophat_SRR036752/ -g 1 -p 4 -C /home/zohra/indexes_bowtie/humain_ SRR036752.fastq [Tue Oct 11 13:23:53 2011] Beginning TopHat run (v1.3.2) --- [Tue Oct 11 13:23:53 2011] Preparing output location /tmp/tophat_SRR036752// [Tue Oct 11 13:23:53 2011] Checking for Bowtie index files [Tue Oct 11 13:23:53 2011] Checking for reference FASTA file [Tue Oct 11 13:23:53 2011] Checking for Bowtie Bowtie version: 0.12.7.0 [Tue Oct 11 13:23:53 2011] Checking for Samtools Samtools Version: 0.1.18 [Tue Oct 11 13:23:53 2011] Generating SAM header for /home/zohra/indexes_bowtie/humain_ [Tue Oct 11 13:23:55 2011] Preparing reads format: fastq quality scale: phred33 (default) [FAILED] Error running 'prep_reads' Error: qual length (51) differs from seq length (51) for fastq record ! * Can you help me. Thanks Zohra Saci ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] tophat error
Hi Zohra, One more bit of help: in the past our team has noticed that Color Space files from NCBI's SRA database have a placeholder adapter base quality score added in (for an unknown reason). If you choose to use Galaxy, when passing the file through the FASTQ Groomer tool (with input and output type set to cssanger) this extra score is removed. This standardizes the data and makes it useable with analysis tools such as Bowtie/TopHat. The same thing could be done on the command line (removing the initial qual score for each FASTQ entry) if that is an option for you. Best wishes for your project, Jen Galaxy team On 10/11/11 12:14 PM, Jennifer Jackson wrote: Hello Zohra, For command line (not Galaxy) use of this tool, questions would be best directed to the tool authors at tophat.cuffli...@gmail.com. That said, there appears to be a mismatch between the quality scores in your fastq file and what was expected (integer, linked to the -C option). Should you decide to use Galaxy at http://usegalaxy.org, there are tools to format the input and run this type of job. To help you get started, please see our tutorial covering this exact type of analysis: http://wiki.g2.bx.psu.edu/Learn/Screencasts see Examples of other analyses - SOLiD Single End Hopefully one of these options will work out for you, Best, Jen Galaxy team On 10/11/11 7:47 AM, zohra saci wrote: Hello, I was trying to run tophat v1.3.2 on SOLID data and I have this error: *zohra@bart:~/Bureau/cancer$ tophat -o /tmp/tophat_SRR036752/ -g 1 -p 4 -C /home/zohra/indexes_bowtie/humain_ SRR036752.fastq [Tue Oct 11 13:23:53 2011] Beginning TopHat run (v1.3.2) --- [Tue Oct 11 13:23:53 2011] Preparing output location /tmp/tophat_SRR036752// [Tue Oct 11 13:23:53 2011] Checking for Bowtie index files [Tue Oct 11 13:23:53 2011] Checking for reference FASTA file [Tue Oct 11 13:23:53 2011] Checking for Bowtie Bowtie version: 0.12.7.0 [Tue Oct 11 13:23:53 2011] Checking for Samtools Samtools Version: 0.1.18 [Tue Oct 11 13:23:53 2011] Generating SAM header for /home/zohra/indexes_bowtie/humain_ [Tue Oct 11 13:23:55 2011] Preparing reads format: fastq quality scale: phred33 (default) [FAILED] Error running 'prep_reads' Error: qual length (51) differs from seq length (51) for fastq record ! * Can you help me. Thanks Zohra Saci ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] TopHat--BAM merge
Hi Rich, Are you using a local instance or the main public instance at http://usegalaxy.org? There was a bug fix to this tool on the public instance right around the time this error was reported. Please try the job again. If it fails, it may be that the files are too large, although an error would be expected. If after the re-run, the same thing occurs, please share a link to the history and we can take a look. Use Options - Share or Publish, generate the link, and send directly to me (not the list). Best, Jen Galaxy team On 9/30/11 9:43 AM, Richard Mark White wrote: Hi, I mapped two illumina runs using TopHat (they are from same RNA sample). Then tried to use the BAM merge tool to make this into one BAM file for further processes. But it returned an empty file. Is this not possible? Maybe I am not understanding the purpose/use of BAM merge? Rich ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] TopHat--BAM merge
Hi, I mapped two illumina runs using TopHat (they are from same RNA sample). Then tried to use the BAM merge tool to make this into one BAM file for further processes. But it returned an empty file. Is this not possible? Maybe I am not understanding the purpose/use of BAM merge? Rich ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Tophat error: broken pipe
Hi Song, We have alpha support for Tophat v1.3.0 and it appears to work fine with Galaxy's Tophat wrappers. We'll upgrade and start full testing near term. For now, when running in a local instances, we do encourage users to try it and see if it meets their needs. Perhaps try with an uncompressed version of the same input file and see if that functions as expected or if the same error is given when used with the Galaxy wrappers? If you want to post testing details (Galaxy pull # from bitbucket, gzip, OS version and anything else you feel is relevant) after this sort of testing, the development team will use that information when full integration testing is performed. Perhaps others running local instances will also comment if you post these detailed testing results to the galaxy-...@bx.psu.edu mailing list (will reach the primary external Galaxy development community). Thanks for using Galaxy! Jen Galaxy team On 7/20/11 6:59 AM, Song Li wrote: Hi Jen, Thank you for the fast reply, however, tophat works fine with this command when used as stand alone software. I checked the version of gzip and it's the same on galaxy server and on the machine where I run tophat alone. The broken pipe error is likely due to a file that is not closed by a previous step. Have anyone tested tophat 1.3 on galaxy? Thanks, Song On Tue 07/19/11 6:45 PM , Jennifer Jackson j...@bx.psu.edu wrote: Hello Song Li, The file extension seems to be a mismatch. file.gz - gzip utility Exploring the use of gunzip or zcat are options to restore a file.z. Hopefully this helps, Jen Galaxy team On 7/19/11 11:52 AM, Song Li wrote: Hello everyone, I was trying to run tophat in a local version of galaxy, but I got the following error: gzip: stdout: Broken pipe [Tue Jul 19 14:10:36 2011] Processing bowtie hits Error: could not open pipe gzip -cd ./tophat_out/tmp/left_kept_reads_missing.fq.z It seems that when tophat is calling gzip, the pipe can not be open. Can anyone suggest a fix to this problem? Thanks, Song Li -- Postdoctoral Associate Uwe Ohler Laboratory Institute for Genome Sciences and Policy 101 Science Drive CIEMAS 2171 Phone: 919-68-2124 Duke University ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev parse.php?redirect=a href=http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ parse.php?redirect=a href=http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org/ parse.php?redirect=a href=http://usegalaxy.org/ http://galaxyproject.org/ parse.php?redirect=a href=http://galaxyproject.org/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev parse.php?redirect=a href=http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ parse.php?redirect=a href=http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org/ http://galaxyproject.org/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] Tophat error: broken pipe
Hello everyone, I was trying to run tophat in a local version of galaxy, but I got the following error: gzip: stdout: Broken pipe [Tue Jul 19 14:10:36 2011] Processing bowtie hits Error: could not open pipe gzip -cd ./tophat_out/tmp/left_kept_reads_missing.fq.z It seems that when tophat is calling gzip, the pipe can not be open. Can anyone suggest a fix to this problem? Thanks, Song Li -- Postdoctoral Associate Uwe Ohler Laboratory Institute for Genome Sciences and Policy 101 Science Drive CIEMAS 2171 Phone: 919-68-2124 Duke University ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Tophat error: broken pipe
Hello Song Li, The file extension seems to be a mismatch. file.gz - gzip utility Exploring the use of gunzip or zcat are options to restore a file.z. Hopefully this helps, Jen Galaxy team On 7/19/11 11:52 AM, Song Li wrote: Hello everyone, I was trying to run tophat in a local version of galaxy, but I got the following error: gzip: stdout: Broken pipe [Tue Jul 19 14:10:36 2011] Processing bowtie hits Error: could not open pipe gzip -cd ./tophat_out/tmp/left_kept_reads_missing.fq.z It seems that when tophat is calling gzip, the pipe can not be open. Can anyone suggest a fix to this problem? Thanks, Song Li -- Postdoctoral Associate Uwe Ohler Laboratory Institute for Genome Sciences and Policy 101 Science Drive CIEMAS 2171 Phone: 919-68-2124 Duke University ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org/ http://galaxyproject.org/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] Tophat error
Hi. Newbie here. I'm trying to setup tophat for our local install. I'm getting the following error when I try to run it. Has anyone seen this before or have any ideas what I can try to fix it. Thanks, Simon Error in tophat: [Wed Jun 29 11:54:09 2011] Beginning TopHat run (v1.3.1) --- [Wed Jun 29 11:54:09 2011] Preparing output location ./tophat_out/ [Wed Jun 29 11:54:09 2011] Checking for Bowtie index files [Wed Jun 29 11:54:09 2011] Checking for reference FASTA file Warning: Could not find FASTA file /var/folders/f1/f1aTv8DnERiCv5ic7O3rlk++-+6/-Tmp-/tmpe7Oa0l/dataset_127234.dat.fa [Wed Jun 29 11:54:09 2011] Reconstituting reference FASTA file from Bowtie index Executing: /Volumes/storagepool/oconnorlab/galaxy_dist/bin/bowtie-inspect /var/folders/f1/f1aTv8DnERiCv5ic7O3rlk++-+6/-Tmp-/tmpe7Oa0l/dataset_127234.dat ./tophat_out/tmp/dataset_127234.dat.fa [Wed Jun 29 11:54:09 2011] Checking for Bowtie Bowtie version: 0.12.5.0 [Wed Jun 29 11:54:09 2011] Checking for Samtools Samtools Version: 0.1.7 [Wed Jun 29 11:54:09 2011] Generating SAM header for /var/folders/f1/f1aTv8DnERiCv5ic7O3rlk++-+6/-Tmp-/tmpe7Oa0l/dataset_127234.dat [Wed Jun 29 11:54:09 2011] Preparing reads format: fastq quality scale: phred33 (default) Left reads: min. length=17, count=2666051 Warning: short reads (20bp) will make TopHat quite slow and take large amount of memory because they are likely to be mapped to too many places [Wed Jun 29 11:54:27 2011] Mapping left_kept_reads against dataset_127234.dat with Bowtie gzip: stdout: Broken pipe [Wed Jun 29 11:54:27 2011] Processing bowtie hits Traceback (most recent call last): File /Volumes/storagepool/oconnorlab/galaxy_dist/bin/tophat, line 2607, in sys.exit(main()) File /Volumes/storagepool/oconnorlab/galaxy_dist/bin/tophat, line 2566, in main user_supplied_deletions) File /Volumes/storagepool/oconnorlab/galaxy_dist/bin/tophat, line 2256, in spliced_alignment ref_fasta) File /Volumes/storagepool/oconnorlab/galaxy_dist/bin/tophat, line 2000, in junctions_from_segments if left_reads_map != left_seg_maps[0]: IndexError: list index out of range ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] Tophat version
Hi, Just wondering when the tophat portion of Galaxy will be updated? Its currently version 1.1.1 and there is now a version 1.2.0 (in fact I think there have been 4 updates). Cheers David ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
