[galaxy-user] RNAseq Clostridium butyricum
Hi, I would like to use Galaxy with RNAseq data generated from Clostridium butyricum species. Please, could you include this genome in your list ? Thank you in advance Best regards Benoit HENNUY ___ 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] Operate on genomic intervals
Hi All, I have two files containing multiple scaffolds and their genomic intervals. Now I want to substract the intervals of one file from the other, but apparently this tool is only available if all the data in the chromosome column have the same name. Does anybody known a way how to handle files with different names in the chromosome column? Thanks a lot in advance, Sarah ___ 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] how to merge multiple fastq files
Hello Kevin, This particular function is like a cat - will work any text file. Assuming that you run the function in the same order the data was split, it should merge fine. Should you want to work with tools that manipulate FASTQ files specifically, a tool search of FASTQ will bring up most plus look under the tool group NGS: QC and manipulation - Generic FASTQ manipulation. And in case you didn't see this, data can be uploaded using FTP. Several compressed formats are support. Using a desktop client can the track progress of, restart, and confirm a load. http://galaxyproject.org/wiki/Learn/Upload%20via%20FTP Best wishes for your project, Jen Galaxy team On 10/27/11 9:01 PM, Kevin Lam wrote: Hi Jennifer, just out of curiousity, is the command a linux cat? or does it actually parse the fastq sequences? asking as my service provider actually just split my PE files by lines (not no. of reads ) in fastq assuming that I can't merge them in galaxy, I am merging them properly then splitting them again (anyway i can map using concurrent processes and merged the bam later on Cheers Kevin On Fri, Oct 28, 2011 at 10:30 AM, Jennifer Jackson j...@bx.psu.edu mailto:j...@bx.psu.edu wrote: Hi Tracy, The tool Text Manipulation - Concatenate datasets tail-to-head can put the two together. Then set the datatype to fastq, if needed (click on the pencil icon for the full dataset to reach the Edit Attributes form to make the change). Be sure to watch out for an extra newline being added between the two files. You can test for/eliminate this using Filter and Sort - Select with the options that: NOT Matching and the pattern: ^$. (the regular expression '^$' [no quotes] matches empty lines). I am sending to the galaxy-user mailing list for our internal tracking and for other users to learn from. Please send all questions directly to the list going forward, it is very helpful for us. Thanks for using Galaxy! Jen Galaxy team On 10/27/11 11:58 AM, Qingquan Liu wrote: Hi Jennifer, I have sequenced one sample on 2 lanes of GAII, and now I am trying to merge the 2 fastq files. How should I do it on Galaxy? Thank you very much! Best, Tracy -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/__Support 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 http://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 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] get data through FTP site
Hi, I faced a similar problem with getting data into history, I tried directly and via FTP. Both cases, the files being loaded to history ended up being incompleted. The upload to FTP was OK. My files were .bzip2. Cheers, Bruno De: galaxy-user-boun...@lists.bx.psu.edu [galaxy-user-boun...@lists.bx.psu.edu] Em Nome De Jennifer Jackson [j...@bx.psu.edu] Enviado: quinta-feira, 27 de Outubro de 2011 21:23 Para: Benoit HENNUY Cc: galaxy-u...@bx.psu.edu Assunto: Re: [galaxy-user] get data through FTP site Hello, Please try an alternate name/compression format. The de tails for supported file names (no spaces) and compression types (.gzip, .bz, bzip2, and single-file .zip) are here: http://galaxyproject.org/Learn/Upload%20via%20FTP Please let us know if we can help again, Best, Jen Galaxy team On 10/26/11 6:25 AM, Benoit HENNUY wrote: Hello, I uploaded (on Oct, 25) data through FTP site and I was not able to retreiven them to include them in a history. I suppose that the files should appeared in the FTP list under the Get data page. THese data are named P2 fastq .gz files that I wold like to use in RNA Seq workflow. Thank you to help me to be able to use these data. Best regards, Benoit HENNUY GIGA Genomics University of Liege Belgium ___ 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 University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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] GATK
Hi Danny, On 10/28/11 8:53 AM, Muehlschlegel, Jochen D.,M.D. wrote: Hi Jen, Great. I am uploading data right now and will try it. It would be a great addition if it worked and I will give you feedback. On another note, is Galaxy in the meantime able to do a cufflinks, specifically Cuffdiff analysis, on paired-end data ? Yes, this options is included on the CuffDiff tool form as an option. Paired vs mate paired data questions would be best directed to the tool authors at tophat.cuffli...@gmail.com. Best, Jen Galaxy team Thanks Danny On 10/27/11 4:56 PM, Jennifer Jacksonj...@bx.psu.edu wrote: Hi Danny, A beta GATK pipeline is available on our Test instance at: http://test.g2.bx.psu.edu/ Feedback about the tool suite is welcomed! Best, Jen Galaxy team On 10/27/11 1:08 PM, Muehlschlegel, Jochen D.,M.D. wrote: Hi, Do you host GATK on the Galaxy server? If not, is there a way to call SNPs from NGS (RNA-seq) data using Galaxy ? Thanks Danny The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ 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 -- 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] Operate on genomic intervals
Hi Sarah, If you just want to compare rows between two files without interpreting genome positional information (similar to the unix comm command), then please see the tools under Join, Subtract and Group. In particular, Subtract Whole Dataset, but perhaps also Compare two Datasets. You will likely need to convert the datatype to be tabular before using the Compare function. Do this by using the Edit Attributes - Change data type form, located by click on the pencil icon in the top right corner of a dataset's box in the history panel. The instructions in the Compare tool form state to use Text Manipulation-Convert, but if your file is already in interval format, a specific type of tabular data, then this is not an appropriate (or needed) step. Hopefully this helps! Best, Jen Galaxy team On 10/28/11 8:19 AM, Sarah wrote: Hi All, I have two files containing multiple scaffolds and their genomic intervals. Now I want to substract the intervals of one file from the other, but apparently this tool is only available if all the data in the chromosome column have the same name. Does anybody known a way how to handle files with different names in the chromosome column? Thanks a lot in advance, Sarah ___ 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] RNAseq Clostridium butyricum
Hello, The quickest way to use this genome is to load it into your history in fasta format. Use FTP, as described here: http://wiki.g2.bx.psu.edu/Learn/Upload%20via%20FTP Then, use the NGS: RNA Analysis tool set's first step TopHat with the option Will you select a reference genome from your history or use a built-in index?: Use one from the history. Most of Galaxy's mapping tools have this option, although it may be named slightly differently on the tool forms. A double check that your uploaded reference genome has the same exact identifiers present in any reference annotation GTF file you plan to use in later steps is a good idea. This will ensure that the TopHat mapping results will be interpreted correctly by the Cuff* tools. Even minor differences in chromosome/scaffold names will cause problems and it is easier to align the naming conventions up-front. Tutorial and FAQ: http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq Best wishes for your project, Jen Galaxy team On 10/28/11 7:38 AM, Benoit HENNUY wrote: Hi, I would like to use Galaxy with RNAseq data generated from Clostridium butyricum species. Please, could you include this genome in your list ? Thank you in advance Best regards Benoit HENNUY ___ 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] Names for genes in RNA-Seq analysis
Hello Olivier, When deleting data, it takes the server a short amount of time to refresh. It may take a bit longer right now since many people are performing this action at the same time. For the RNA-seq analysis question, reference annotation GTF files are used by the Cuff* programs. (These are different than the result GTF files produced by the programs). For reference annotation GTF files, there are many sources, including Ensembl and UCSC. Here are links to a tutorial and an FAQ that can help with your usage question. http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq But, there are many small details to running the tools to get the optimal results. These types of questions concerning functionality are best directed to the tool authors at tophat.cuffli...@gmail.com Take care, Jen Galaxy team On 10/25/11 11:24 PM, GANDRILLON OLIVIER wrote: Hello Jennifer Le 26/10/11 02:15, « Jennifer Jackson »j...@bx.psu.edu a écrit : Hello Olivier, Are you using a reference gene annotation GTF file? Well if I do , I do not know :-) What I used is first TopHat and then Cufflink. At what stage shall I use such a GTF file? And additionnaly: where shall I find such a GTF file? As I understand it: there are tow sources for a GTF file: 1. The output from cufflinks generates one (but there is no gene names in it..) 2. I could get one from Ensembl? Shall I then use Cuffcompare on the cufflink output? Best Olivier PS: I am now stuck with the galaxy websute that state that I am over my disk quota. I have deleted a couple of files but this does not seems to help... -- 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-dev] Importing existing data into Galaxy
Data libraries are accessible from the Shared Data pop-up menu in the top Galaxy menu bar. On Oct 28, 2011, at 1:12 PM, Oren Livne wrote: Dear Greg, Thanks so much, this helps a lot. I created a public data library, but it is not listed in the list of libraries on the left pane in Analyze Data. How can I access it and use its files in workflows? Oren On 10/27/2011 7:55 PM, Greg Von Kuster wrote: Oren, The best way to do this would be to use galaxy data libraries, uploading files from file system paths and not copying the files into the Galaxy file location. The following provides all of the details about data libraries: http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Libraries The following provides specific details about the various options for uploading files to data libraries. http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files Let us know if you encounter any issues. Greg Von Kuster On Oct 27, 2011, at 4:31 PM, Oren Livne wrote: Dear All, We have a large collection of large data files on our shared file system. We would like to make a subset of them available to a galaxy user session (based on user privileges; different subsets for different users). We want to leave files in their original locations and point galaxy to their paths without copying them. What is the best option for implementing this bridge? Remote data source/data library uploaded on the fly/other? Thanks, Oren ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ Greg Von Kuster Galaxy Development Team g...@bx.psu.edu Greg Von Kuster Galaxy Development Team g...@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] [galaxy-dev] Importing existing data into Galaxy
Dear Greg, Thanks so much, this helps a lot. I created a public data library, but it is not listed in the list of libraries on the left pane in Analyze Data. How can I access it and use its files in workflows? Oren On 10/27/2011 7:55 PM, Greg Von Kuster wrote: Oren, The best way to do this would be to use galaxy data libraries, uploading files from file system paths and not copying the files into the Galaxy file location. The following provides all of the details about data libraries: http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Libraries The following provides specific details about the various options for uploading files to data libraries. http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files Let us know if you encounter any issues. Greg Von Kuster On Oct 27, 2011, at 4:31 PM, Oren Livne wrote: Dear All, We have a large collection of large data files on our shared file system. We would like to make a subset of them available to a galaxy user session (based on user privileges; different subsets for different users). We want to leave files in their original locations and point galaxy to their paths without copying them. What is the best option for implementing this bridge? Remote data source/data library uploaded on the fly/other? Thanks, Oren ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ Greg Von Kuster Galaxy Development Team g...@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] (no subject)
Dear All How can I de-subscribe from the mailing list? Any help would be appreciated Kind Regards M. 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/
[galaxy-user] how to manage mailing list subscriptions
Hello, I have removed you from galaxy-user. Instructions to manage list membership is at the bottom of this and all mailing list messages. In short, through this link: http://lists.bx.psu.edu/ Or request help from this email: galaxy-user-ow...@lists.bx.psu.edu. Is best not to post to the mailing list for this sort of request, especially not as a reply to another thread. Thanks, Jen Galaxy team On 10/28/11 12:49 PM, Mahjoubeh Jalali wrote: Dear All How can I de-subscribe from the mailing list? Any help would be appreciated Kind Regards M. 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 ___ 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] how to transfer gene id into protein id
Hi, I have some refseq gene id, like NM_* and NR_**. I know how to transfer NM_** into protein ID NP_*. But, how to transfer NR_* into protein id, like NP_? I do not know. Could you please tell me? Thank you very much! Victor From: Jennifer Jackson [j...@bx.psu.edu] Sent: Thursday, October 27, 2011 11:23 PM To: Li, Jilong (MU-Student) Cc: galaxy-u...@bx.psu.edu Subject: Re: [galaxy-user] how to transfer gene id into protein id Hello, If the reference genome is in UCSC and has a RefSeq track, then you can extract a file with the transcript and protein identifiers from the Table Browser called refLink and subset it for rows in your query RefSeq transcript identifiers. If the RefSeq data is at BioMart or another source, a similar path to the one I outline below will work with some modifications, it all depends on the file format, but Galaxy's tools can manipulate data is just about every way you will need. Using a transcript identifier query, subset protein identifiers in a UCSC RefSeq track: A. Load your list of NM* identifiers (Get Data - Upload). - set the file format to tabular (use pencil icon to Edit Attributes - Change data type) if needed. B. Load RefSeq id mapping data with Get Data - UCSC Main and set the form parameters as needed, choosing the track RefSeq Genes and the table refLink. Make sure the region is the entire genome. Send to Galaxy formatted as-is (tabular). B. Next, cut columns 3 and 4 out of the table with tool Text Manipulation -Cut and the options c3,c4. C. OPTIONAL, if you want the full list of coding RefSeqs for another purpose... remove the non-coding RefSeqs with the tool Filter and Sort - Select and the options that: NOT Matching and the pattern: ^NR_.*$. Be sure to enter the regular expression '^NR_.*$' without any quotes. D. Perform a join using Join, Subtract and Group - Compare two Datasets with the options: - Compare: file of trans and prot id, filtered or not - Using column: c1 where c1 is the trans ids - against: file of trans ids - and column: c1 where c1 is the trans ids - To find: Matching rows of first dataset E. Result dataset is a two column tabular file: transcript id tab protein id Hopefully this helps you and others who are doing a similar task. If you think you will be doing this a lot, be sure to consider extracting the steps into a workflow. Thanks for using Galaxy, Jen Galaxy team On 10/27/11 1:34 PM, Li, Jilong (MU-Student) wrote: Hi, I have some refseq gene id, like NM_*. How can I transfer these gene id into protein id, like NP_? Thank you very much! Victor ___ 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/
