November 2011 - galaxy-user - lists.galaxyproject.org

Genome database/builds missing?
by Daniel N. Hupalo 02 Nov '11

02 Nov '11

I've been using galaxy to analyze maf files and today the drop down list for database/builds for genomes has lost most of the genomes once listed. I no longer see any bacteria or plants on the list, specifically TAIR9 arabidopsis is no longer on the drop down list when it was just yesterday. Did something change? Thanks - Dan

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Dataset not appearing as available input to SAM analyses
by James Nelson 02 Nov '11

02 Nov '11

Hi, I'm trying to use the SAM/Filter pileup analysis on some pileup output files I've uploaded. But when I click the analysis link, these output files don't appear in the Select dataset dropdown menu; instead only one file, the output from FASTQ Summary Statistics which is obviously not pileup output, is shown. Thanks Clare Nelson

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RNA-seq with Staphylococcus aureus strain Newman
by Joe J Harrison 02 Nov '11

02 Nov '11

Hello, Would you please add Staphylococcus aureus strain Newman to your database? Workflows to analyze data for genomes available through your database are really simple - but I must admit that I've been struggling with trying to get this to work for a genome (and in particular with the annotation) that I've uploaded myself. Thanks for the help and the continued support! Joe ---- Joe J. Harrison Senior Fellow Department of Microbiology University of Washington

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Re: [galaxy-user] RNAseq Helicobacter pylori
by Jennifer Jackson 02 Nov '11

02 Nov '11

Hello Kaisa, These are related formats and generally differ only in the 9th column, which is important for data labeling with these tools. The formats as well as some utilities to help with parsing are documented here: http://cufflinks.cbcb.umd.edu/gff.html Also note the help email: tophat.cufflinks(a)gmail.com For the data files in GFF, you may try contacting the data source and asking for help. It is possible that the attributes needed to create a GTF file exist in other files and the data could be transformed (outside of Galaxy). Hopefully this helps, Jen Galaxy team On 11/2/11 4:58 AM, Kaisa Thorell wrote: > Hi! > > I tried to do as you described but when I come to the tophat/cufflinks analysis I can only find .gff files for the strains that I'm working with and no .gtf files. What is the difference between them and is there any way to convert the .gff into .gtf or does one need any additional information? > > Best regards > > Kaisa > > ________________________________________ > From: galaxy-user-bounces(a)lists.bx.psu.edu [galaxy-user-bounces(a)lists.bx.psu.edu] on behalf of Jennifer Jackson [jen(a)bx.psu.edu] > Sent: 28 October 2011 19:42 > To: Benoit HENNUY > Cc: galaxy-user(a)bx.psu.edu > Subject: 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/ > -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support

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