Re: [galaxy-user] Samtools Mpileup output
On Wed, Nov 6, 2013 at 12:08 PM, Fabrice Besnard fbesn...@biologie.ens.fr wrote: Would you have any advice to select the output format, or alternatively, a tool in Galaxy that can convert pileup into .vcf? Hi Fabrice, I believe you only get the BCF output when Genotype Likelihood Computation is set to Perform genotype likelihood computation. Hope it helps, Carlos ___ 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] Secure file upload gateway for Galaxy
On Tue, Sep 24, 2013 at 7:58 AM, Georgios Magklaras georg...@biotek.uio.no wrote: Hi, Do you have best recipes for SFTP/Aspera upload gateway integration to Galaxy? We would welcome advise on that matter. Hi, I haven't implemented yet, but I'm planning on using plain scp(windows user can use WinSCP). I shouldn't have problems doing so by using this option in universe_wsgi.ini: # Add an option to the library upload form which allows authorized # non-administrators to upload a directory of files. The configured directory # must contain sub-directories named the same as the non-admin user's Galaxy # login ( email ). The non-admin user is restricted to uploading files or # sub-directories of files contained in their directory. user_library_import_dir = /local/opt/galaxy/import_dir Hope it helps, Carlos ___ 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] Remove unpaired reads from quality-filtered pared-end fastq files.
Not the most convenient solution, but what I normally do in this situation is to combine the two files, filter then split again. There are tools for combining and splitting paired fastq files in Galaxy. Hope it helps, Carlos On Jan 8, 2013 12:55 AM, 柴田 弘紀 hshib...@gen.kyushu-u.ac.jp wrote: Hi there, I obtained two fastq files from GA paired end run. I filtered each file by quality using fastq tool kit. Then some forward reads may be removed by low quality whereas the reverse counterparts are OK to be remained on the other file, or vice versa. I want to remove those unpaired reads from filtered fastq files so that the two new fastq files contain the identical sets of the reads. Is it possible to do it on galaxy? Thank you very much. Hiroki ___ 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] Installing Galaxy on a Cluster - What to do about Python
On Tue, Nov 6, 2012 at 2:27 PM, greg margeem...@gmail.com wrote: Could anyone provide me with some basic directions on how to set it up with virtualenv? I've never used it before. I do this by adding this to the ~/.bashrc file of the user running galaxy( in galaxy.fedora-init: RUN_AS=galaxy) source $HOME/env/bin/activate Hope it helps, Carlos ___ 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] Are tools must be installed in local machine?
Hi Sachit, Björn answer is correct. The issue is what is a tool. There are what Galaxy calls tools. Some of which are installed by default and some of which you can install from the toolshed. There are in many cases just wrappers to third-party tools that need to be installed and available in the environment PATH of the user running Galaxy. Examples of these are TopHat, Bowtie and BWA. Björn mentions in some cases the third-party tool is automatically installed, but this is new and most third-party tools need to be installed manually still. If you are using Debian, thanks to the Debian Med Team, many tools are already available in the repositories. Both TopHat and Bowtie are. So apt-getting them should do for you. Just remember to configure the .loc files in Galaxy with the location of the index files. This link will be helpful: http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup Hope this helps, Carlos On Mon, Oct 8, 2012 at 6:48 AM, Sachit Adhikari sachit.techner...@gmail.com wrote: I don't think you understood my question very well. Tophat and Bowtie are available by default in Galaxy. Tophat and Bowtie however is not installed in my operating system. Will it still work in Galaxy? On Mon, Oct 8, 2012 at 3:22 PM, Björn Grüning bjoern.gruen...@pharmazie.uni-freiburg.de wrote: Hi Sachit, you need to install such tools by yourself, unless you are using some new tools from the toolshed. For example the ncbi-tools or BWA from the toolshed are capable of installing all dependency automatically. In the future the plan is to move all heavy tools to the toolshed with automatic dependency and version handling, afaik. Regards, Bjoern Hello. The tools like Tophat, Bowtie etc are pre-installed in Galaxy. Are those tools must be installed in order to work in Galaxy. For example: I am using Debian machine(Don't have tophat and bowtie installed). Will tophat and bowtie work in my local galaxy? Thanks ___ 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/
Re: [galaxy-user] Is there web-based CummeRbund?
Hi Jianguang, I'm the author of cummeRbund wrapper in the test Galaxy Tool Shed. I never got around to quite finish it, that's why I never submitted to main. Also cummeRbund received a big update since the time I was writing this wrapper. I don't think I can recommend using the wrapper in its current state at all. In any case, even if the wrapper could help you, you would need to deploy a local or a cloud instance of Galaxy, as is not clear to me that this wrapper would make its way to Galaxy Main server any time soon. You would probably be better of by dealing with R and cummeRbund, which by the way you should be able to use in Windows. If I find the time to play with the cummeRbund Galaxy wrapper again, I'll make sure to comment about it in this list. Best, Carlos On Sat, Aug 25, 2012 at 8:09 PM, Dave Clements cleme...@galaxyproject.org wrote: Hi Jianguang, I went to http://galaxy.psu.edu/search/web/ and searched for cummerbund. It looks like there is a cummerbund wrapper in the test Galaxy Tool Shed, but that is about it. Dave C On Fri, Aug 24, 2012 at 3:23 PM, Du, Jianguang jia...@iupui.edu wrote: Dear All, I am going to visualize Cuffdiff outputs. I understand that CummeRbund can be used to visualize Cuffdiff outputs. However, I am not good at Linux system and feel difficult to understand CummeRbund manual. Is there web-based CummeRbund program (like Tophat and Cufflink) available for use? If web-based CummeRbund does not exist, is there other web-based program can be used to visualize Cuffdiff outputs? Thanks. 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/ -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/ ___ 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] Question about Unified genotyper
Hi Mathew, Regarding 1 you might want to read this thread: http://user.list.galaxyproject.org/Problem-with-Depth-of-Coverage-on-BAM-files-GATK-tools-td4654147.html All tools from GATK are limited to hg_g1k_v37 as far as I know. Best, Carlos On Mon, Aug 6, 2012 at 10:30 AM, Mathew Bunj mathewb...@yahoo.com wrote: I have been trying to use either Unified genotyper or Freebayes on one of the Bam file. Both are failing. 1. With Unified genotyper it give me message saying Sequences are not currently available for specified build. I have hg19 related data and using default settings (pick up hg_g1k_v37 no other option). I am not sure why it is giving me this error. 2. As an alternative I tried to run Freebayes with default setting and choosing hg19 - it i snot giving any specific message but undetr bug icon gives me -killed. Now in order to make sure my Bam is OK, I tested out side Galaxy mPile up and with in Galaxy pile up. Any suggestion why UNified genotyper is not working. If needed I can share my history. Thanks. ___ 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] Getting reference index files in local galaxy install
Also make sure you are using TABs to separate the fields in the .loc file, this has bitten me several time in the past. My vim config places 4 spaces instead of TAB, to deactivate this option you can do :set noexpandtab. Hope it helps, Carlos On Thu, Jul 5, 2012 at 4:39 AM, Avik Datta reach4a...@gmail.com wrote: Hi Aarti, Check the name of your ref file. If it is hg19.fa, then modify loc file as hg19 hg19 HG19_BWA /root/Ref_INDEX/HG19BWAIndex/base/hg19.fa Avik Datta On Thu, Jul 5, 2012 at 1:42 PM, Aarti Desai aarti_de...@persistent.co.in wrote: Hi, We have a local install of galaxy and I’m trying to add the reference index files for bwa using the information provided in the following link http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup I have modified the bwa_index.loc file present in the ../tool-data directory by adding the path to where the index is on our server (Also attached). However, even after restarting the server, the reference genome does not show when choosing the “use a built-in index option”. I’m not sure whether the loc file is correctly created and whether any other configuration file needs to be changed/updated. Help in the matter greatly appreciated. Thanks, Aarti From: galaxy-user-boun...@lists.bx.psu.edu [mailto:galaxy-user-boun...@lists.bx.psu.edu] On Behalf Of Jennifer Jackson Sent: Thursday, July 05, 2012 1:23 AM To: Lindsey Kelly Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] Initial QC and grooming for Illumina HiSeq2000 paired end RNAseq data Hello Lindsey, Yes, you have this correct. The general path would be to: - join forward and reverse data per run - run FASTQ Groomer FastQC (note: if your data is already in Sanger FASTQ format with Phred+33 quality scaled values, the datatype '.fastqsanger' can be directly assigned and the FASTQ Groomer step skipped. This is likely true if your data is a from the latest CASAVA pipeline, but please double check.) - discard data as needed based on quality - split forward and reverse data that passes QC - concatenate all forward reads from a sample into one FASTQ file - concatenate all reverse reads from a sample into one FASTQ file. - for each sample, run TopHat using the two concatenated FASTQ files To manipulate paired end data, please see the tools - NGS: QC and manipulation: FASTQ splitter FASTQ joiner. To combined data files head-to-tail from multiple runs into a single FASTQ file please see the tool - Text Manipulation: Concatenate datasets. I am not sure of the actual volume of data, but if these start to get large or TopHat errors with a memory problem, a local or cluster instance would be the recommendation: http://getgalaxy.org For reference: http://tophat.cbcb.umd.edu/manual.html http://www.nature.com/nprot/journal/v7/n3/full/nprot.2012.016.html Hopefully this helps. Others are welcome to post comments/suggestions. Jen Galaxy team On 7/2/12 11:17 AM, Lindsey Kelly wrote: I am trying to do RNAseq analysis on Paired end data from the Hiseq2000. I have about 50 files for each sample (25 forward and 25 reverse - although each sample has a different number of files). I think that I need to: -convert them into FASTQ sanger format using the FASTSQ groomer tool -check the quality using the FASTQqc tool I don't know how to handle this many files. Do I have to groom and run the QC for each file? Should I join the paired files and run both tools on each pair, or should I combine all of the data for each sample (which I don't know how to do) and then groom and run the QC for all of the reads for the sample. Thanks in advance for advice Lindsey ___ 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 DISCLAIMER == This e-mail may contain privileged and confidential information which is the property of Persistent Systems Ltd. It is intended only for the use of the individual or entity to which it is addressed. If you are not the intended recipient, you are not authorized to read, retain, copy, print, distribute or use this message. If you have received this communication in error, please notify the sender and delete all copies of this message. Persistent Systems Ltd. does not accept any liability for virus infected mails. ___ The Galaxy User list should be
Re: [galaxy-user] Problem with Depth of Coverage on BAM files (GATK tools)
Hi Lilach, Sorry for the late response. Jen just confirmed the disadvantages of my approach. I don't know how difficult could be for you to double check the coordinates you have in your interval file are correct for hg_g1k_v37. If you feel confident they will work and want to proceed, you could do something like this outside of galaxy, you could also I'm sure find a way to do it inside galaxy: sed 's/^chr//' interval_file.csv interval_file_g1k.csv If you have coordinates for the mitochondrial chromosome you might have to do also: sed 's/^MT/M/' interval_file.csv interval_file_g1k.csv As if I remember correctly UCSC uses chrMT and GATK expects just M. Please double check this as I'm not sure. It would be also nice is there were a confirmation on what exactly hg_g1k_v37 is, and where you could find annotations for it. Annotations from Ensembl would do? Regards, Carlos On Mon, Jun 25, 2012 at 5:22 PM, Jennifer Jackson j...@bx.psu.edu wrote: Hello Lilach, Currently, the human reference genome indexed for the GATK-beta tools is 'hg_g1k_v37'. The GATK-beta tools are under active revision by our team, so we expect there to be little to no change to the beta version on the main public instance until this is completed. Attempting to convert data between different builds is not recommended. These tools are very sensitive to exact inputs, which extends to naming conventions, etc. The best practice path is to start and continue an analysis project with the same exact genome build throughout. If you want to use the hg19 indexes provided by the GATK project, a cloud instance is the current option (using a hg19 genome as a 'custom genome' will exceed the processing limits available on the public Galaxy instance). Following the links on the GATK tools can provide more information about sources, including links on the GATK web site which will note the exact contents of the both of these genome versions, downloads, and other resources. Hopefully this helps to clear up any confusion, Best, Jen Galaxy team On 6/21/12 7:50 AM, Lilach Friedman wrote: Hi Jennifer, Thank you for this reply. I made a new BWA file, this time using the hg19(full) genome. However, when I am trying to use DepthOfCoverage, the reference genomr is stucked on the hg_g1k_v37 (this is the only option to select), and I cannot change it to hg19(full). Most probably, because I selected hg_g1k_v37 in the previous time I tried to use DepthOfCoverage. It seems as a bug? How can I change it? Thanks, Lilach 2012/6/18 Jennifer Jackson j...@bx.psu.edu Hi Lilach, The problem with this analysis probably has to do with a mismatch between the genomes: the intervals obtained from UCSC (hg19) and the BAM from your BWA (hg_g1k_v37) run. UCSC does not contain the genome 'hg_g1k_v37' - the genome available from UCSC is 'hg19'. Even though these are technically the same human release, on a practical level, they have a different arrangement for some of the chromosomes. You can compare NBCI GRCh37 with UCSC hg19 for an explanation. Reference genomes must be exact in order to be used with tools - base for base. When they are exact, the identifier will be exact between Galaxy and the source (UCSC, Ensembl) or the full Build name will provide enough information to make a connection to NCBI or other. Sometimes genomes are similar enough that a dataset sourced from one can be used with another, if the database attribute is changed and the data from the regions that differ is removed. This may be possible in your case, only trying will let you know how difficult it actually is with your analysis. The GATK pipeline is very sensitive to exact inputs. You will need to be careful with genome database assignments, etc. Following the links on the tool forms to the GATK help pages can provide some more detail about expected inputs, if this is something that you are going to try. Good luck with the re-run! Jen Galaxy team On 6/18/12 4:42 AM, Lilach Friedman wrote: Hi, I am trying to used Depth of Coverage to see the coverages is specific intervals. The intervals were taken from UCSC (exons of 2 genes), loaded to Galaxy and the file type was changed to intervals. I gave to Depth of Coverage two BAM files (resulted from BWA, selection of only raws with the Matching pattern: XT:A:U, and then SAM-to-BAM) and the intervals file (in advanced GATK options). The consensus genome is hg_g1k_v37. I got the following error message: An error occurred running this job: Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/space/g2main # ERROR -- # ERROR A USER ERROR has occurred (version 1.4-18-g80a4ce0): # ERROR The invalid argume Is it a bug, or did I do anything wrong? I will be grateful for any help. Thanks! Lilach ___ The Galaxy User
Re: [galaxy-user] Help!! Tophat paired end reads
Hi Jennifer, This is a subject I'm interested in. I wonder if you could share a workflow to estimate percentage of reads mapping to for example exomes(I can get the coordinates for a GFF dataset). I have a mapping result for RNA-seq data and by looking in the browser, it seems to also have a lot of reads mapping outside of exomes, but I would like to put numbers on it. Thanks, Carlos P.D. I'm trying now to get GATK's 'Depth of Coverage' to work, but I'm having some issues with it. Is there any other options in Galaxy? On Mon, Apr 16, 2012 at 12:27 AM, Jennifer Jackson j...@bx.psu.edu wrote: Hi Jiwen, The bioinformatics part of your analysis sounds as if it went fine, so that is good news. This list may not be the best place to get feedback about library construction methods, but we can see who has help to offer. I did a quick search myself and found this recent publication that includes a comparison of rRNA depletion methods with mapping profiles: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0027288 Best, Jen Galaxy team On 4/15/12 8:24 AM, 杨继文 wrote: Hi, I am very confused by my mapping. Please help me figure out what's wrong with my operation. I got Illumina Hiseq 2000 paired end reads (mouse), and I used Tophat to map these reads. After mapping, I used IGV to have a look at the mapping. I can see that some of the reads fall into exons or span exons (splice junction). These reads seem to fit very well. However, I can also see a lot reads mapped to non-coding region. Are these reads from pre-mRNA? or my mapping was wrong? Did anybody have similar experience?? Furthermore, I can see huge enrichment of reads in 3' UTR (much much more than the coding region). Is this normal? Is this caused by the rRNA depletion method ? 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/ -- 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/ ___ 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] How can I sort BAM/SAM file by read names?
Hi, I need to sort a BAM file by read names, I was wondering if this is possible with a tool included in Galaxy? I know any BAM file produced inside Galaxy will be sorted by coordinates, but I couldn't find an option to change this to queryname in any tool. Picard has the tool SortSam[1], perfect for this task, but it doesn't seem to be included at the moment. Is there any other option currently included? Are there any plans to include one? [1]http://picard.sourceforge.net/command-line-overview.shtml#SortSam Thanks, Carlos ___ 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/
Re: [galaxy-user] ILLumina 1.9 Hiseq
Hi Jen, I have a related question. If Illumina 1.9 is already in Sanger format, is it still necessary to groom the FASTQ files for TopHat? Would it be enough to directly change the data type to Sanger without grooming? Thanks, Carlos On Wed, Feb 29, 2012 at 10:57 AM, Jennifer Jackson j...@bx.psu.edu wrote: Hello, The input quality score type should be set as Sanger for your data. Thanks! Jen Galaxy team On 2/29/12 7:39 AM, Ateequr Rehman wrote: Dear Glaxy users and admin I ran my sequence data on FASTQC tool, output says it is Encoding Sanger / Illumina 1.9 now i want to groom my file, but groomer does not have option for 1.9 in Input FASTQ quality scores type any idea which option i should select to grroom my file, later i want to run Bowtie or Tophat, Thanks ** ___ 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/ ___ 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] Solution for: Error running cuffdiff. Error: cannot open reference GTF file CONDITION, CONTROL for reading
Hi, I ran into this error running cuffdiff. I had a hard time debugging this user error, so I though it would be nice to share the solution. This was in a local instance, but I don't see why it wouldn't happen in Galaxy Main under the same circumstances. Tool execution generated the following error message: Error running cuffdiff. Error: cannot open reference GTF file CONDITION,CONTROL for reading The tool produced the following additional output: cuffdiff v1.3.0 () cuffdiff --no-update-check -q -p 4 -c 1000 --FDR 0.05 -N -b --labels CONDITION,CONTROL /local/db/genomes/illumina/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf /local/opt/galaxy_central/database/files/001/dataset_1339.dat,/local/opt/galaxy_central/database/files/001/dataset_1391.dat /local/opt/galaxy_central/database/files/001/dataset_1452.dat,/local/opt/galaxy_central/database/files/001/dataset_1478.dat The problem ended being the use of Perform Bias Correction(-b) and a GTF file with no Database/Build associated. Looking at cuffdiff wrapper I found, if a FASTA reference is not selected from the history, the FASTA reference of the GTF file associated build is used. If there is not build association, your cuffdiff run will fail with this not so helpful error. My feeling is, cuffdiff should check for a non-dashed string after '-b' and complain if is absents, but this doesn't happen currently. Kind regards, Carlos ___ 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] Sort sam or bam
Hi Claire, Your welcome!. If you feel it could be helpful, this is what I have so far as a workflow for GATK: http://test.g2.bx.psu.edu/u/cjav/w/gatk Is not complete, but I think it could be a good starting point. Please if you ended using this workflow as a starting point and find something you think it could be improve, let me know. There are things like which annotations or ROD file I should use, that I haven't been able to quite understand. Regards, Carlos On Mon, Jan 23, 2012 at 7:44 AM, Clare Sloggett s...@unimelb.edu.au wrote: Hi Carlos, Thanks! I didn't realise the conversion was doing that. In fact I want bam files (I'm also using GATK) so this is really helpful. Cheers, Clare On Thu, Jan 19, 2012 at 2:32 AM, Carlos Borroto carlos.borr...@gmail.com wrote: Hi Clare, I ran into a similar question testing out GATK pipeline on Galaxy. My solution was to always convert my SAM files to BAM. The wrapper also sorts the final BAM file output and it does this using the known 'samtools sort', which sorts chromosomes in the same order of the reference genome. The reference genome can be automatically selected by the build associated with the dataset or choose from the history. I haven't confirmed if a conversion from BAM to SAM would do the same thing. Hope it helps, Carlos On Wed, Jan 18, 2012 at 12:00 AM, Clare Sloggett s...@unimelb.edu.au wrote: Hi Jen, Thanks for this, belatedly! And happy new year! I think this will work for some of my cases but possibly not all, since it looks like chromosomes are being sorted alphabetically. It depends what the reference genome used was and what tools you're planning to use after sorting as to whether this is ok. I was initially just wondering why 'samtools sort' hadn't been wrapped - not as a complaint, but since the various other samtools options mostly seem to be already wrapped, I wondered if there was some particular reason not to have this one. If I were to try to wrap 'samtools sort' myself is there some difficulty I should know about? Thanks again, Clare On Wed, Dec 7, 2011 at 4:24 AM, Jennifer Jackson j...@bx.psu.edu wrote: Hello Clare, An example of how to sort a SAM file is included in the workflow from #2 on this FAQ (it can be imported and the sort modified as needed): http://usegalaxy.org/u/jeremy/p/transcriptome-analysis-faq If you are starting with a BAM file, convert BAM-SAM, then after sorting, back with SAM-BAM, using tools in the group NGS: SAM Tools. Best regards, Jen Galaxy team On 12/4/11 9:45 PM, Clare Sloggett wrote: Hi galaxy users, Am I right in thinking there is no tool for sorting a sam/bam file in Galaxy? I think this has probably been discussed before, sorry. I just want to check I haven't missed anything, since sibling tools from e.g. the samtools and picard suites are wrapped. Thanks, Clare -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support -- E: s...@unimelb.edu.au P: 03 903 53357 M: 0414 854 759 ___ 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/ -- E: s...@unimelb.edu.au P: 03 903 53357 M: 0414 854 759 ___ 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] Galaxy test won't run a bwa job
Hi, I'm trying to test a workflow using tools only available on the test server, for this I have uploaded a limited subset of my data that should run fairly quickly. The first step is a BWA mapping, but the job has being in the queue since yesterday. Is it fine to run this kind of test there? Thanks, Carlos ___ 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] Galaxy test won't run a bwa job
Hi Jen, I did as you recommended a rerun my job, but after 2hrs is still waiting. This is my history if that helps: http://test.g2.bx.psu.edu/u/cjav/h/gatk---hg19---example Regards, Carlos On Tue, Nov 22, 2011 at 12:30 PM, Jennifer Jackson j...@bx.psu.edu wrote: Hello Carlos, The NGS cluster was down yesterday for maintenance. Restarting the BWA job should initiate the run. Hopefully this helps, Jen Galaxy team On 11/22/11 7:56 AM, Carlos Borroto wrote: Hi, I'm trying to test a workflow using tools only available on the test server, for this I have uploaded a limited subset of my data that should run fairly quickly. The first step is a BWA mapping, but the job has being in the queue since yesterday. Is it fine to run this kind of test there? Thanks, Carlos ___ 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] Galaxy test won't run a bwa job
Thanks Mike, that's what I ended doing. On Tue, Nov 22, 2011 at 4:32 PM, Mike Dufault dufau...@yahoo.com wrote: Hi Carlos, You can always run your BWA on the Main Galaxy and then import the data directly into the Test Galaxy using the http: address; no need to download to your local machine. The http: address can be found by by selecting properties on the disk icon. Instead of downloading, you can just copy the http:. I hope this helps, Mike --- On *Tue, 11/22/11, Carlos Borroto carlos.borr...@gmail.com* wrote: From: Carlos Borroto carlos.borr...@gmail.com Subject: Re: [galaxy-user] Galaxy test won't run a bwa job To: Jennifer Jackson j...@bx.psu.edu Cc: galaxy-user@lists.bx.psu.edu Date: Tuesday, November 22, 2011, 3:12 PM Hi Jen, I did as you recommended a rerun my job, but after 2hrs is still waiting. This is my history if that helps: http://test.g2.bx.psu.edu/u/cjav/h/gatk---hg19---example Regards, Carlos On Tue, Nov 22, 2011 at 12:30 PM, Jennifer Jackson j...@bx.psu.eduhttp://mc/compose?to=j...@bx.psu.edu wrote: Hello Carlos, The NGS cluster was down yesterday for maintenance. Restarting the BWA job should initiate the run. Hopefully this helps, Jen Galaxy team On 11/22/11 7:56 AM, Carlos Borroto wrote: Hi, I'm trying to test a workflow using tools only available on the test server, for this I have uploaded a limited subset of my data that should run fairly quickly. The first step is a BWA mapping, but the job has being in the queue since yesterday. Is it fine to run this kind of test there? Thanks, Carlos ___ 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/ ___ 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] How to use GATK Unified Genotyper with A list of genomic intervals over which to operate option
Hi, I would like to run Unified Genotyper on a region of a BAM file, I see the advance option A list of genomic intervals over which to operate exist and seems to be what I need. The problem is I only get a drop-down menu with the single option Selection is optional, which I don't understand. Thanks, Carlos ___ 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] Xgrid and Galaxy
Hi Paul, If you manage to get Xgrid working with galaxy, please share your success, as I would love to try it. But know that you can use SGE on Mac OS X. I was able to get it working by following this blog post and screencast: http://www.bioteam.net/2010/02/grid-engine-6-2-on-mac-os-x/ I tried to compile SGE by myself, but couldn't, so I used this binaries: http://biote.am/sge/ --Carlos On Fri, Aug 19, 2011 at 4:14 AM, Roman Valls brainst...@nopcode.org wrote: I'm no expert on MacOS but since Xgrid seems to have an opensource DRMAA implementation, it *might* be possible (with some integration/programming efforts): http://edbaskerville.com/2006/08/22/xgriddrmaa-011-with-examples/ This blog author might help you if you run into issues.. Hope that helps ! On 2011-08-16 22:26, Paul Cantalupo wrote: Hello, I'm trying to determine if Galaxy will work with Xgrid to set up a small cluster of Mac's for next-gen sequencing projects. I saw on http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server that Galaxy supports Torque PBS or Sun Grid. I don't think that Sun Grid runs on Snow Leopard and I don't know about Torque. Snow Leopard already comes with Xgrid so I was hoping to use it. Thank you for your help, Paul Cantalupo University of Pittsburgh ___ 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] Unable to queue tophat's job for execution
Hi, The main Galaxy server is failing to schedule tophat's jobs. Giving error: Unable to queue job for execution. Resubmitting the job may succeed. I've been able to run other tools jobs. Thanks, Carlos ___ 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] Unable to queue tophat's job for execution
This problem went away. Thanks. On Tue, Aug 9, 2011 at 10:55 AM, Carlos Borroto carlos.borr...@gmail.com wrote: Hi, The main Galaxy server is failing to schedule tophat's jobs. Giving error: Unable to queue job for execution. Resubmitting the job may succeed. I've been able to run other tools jobs. Thanks, Carlos ___ 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/
