- galaxy-user - lists.galaxyproject.org

Expected Transcriptome BLAST
by Colicchio, Jack M 02 Nov '11

02 Nov '11

Hey, Jack Colicchio here, a PhD. student at KU. I am about to get an illumina Next gen transcriptome data setthat I would like to align and quantify against a list of expected transcripts from Mimulus guttatus. The expected transcripts are in .gff format, and I was wondering how I could get that file uploaded to you're website to allow me to align my transcriptome against. I successfully uploaded the .GFF file, and can view it on your site, but do not know how I could blast my .fastq data from illumine against this file. Thanks, Jack

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Re: [galaxy-user] Names for genes in RNA-Seq analysis
by Jennifer Jackson 02 Nov '11

02 Nov '11

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.cufflinks(a)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 »<jen(a)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

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Cannot get rid of custom build error
by James Vincent 02 Nov '11

02 Nov '11

Hello, I've tried to create a custom build (starting from the trackster page) and clearly made some mistake. I get a NoConverterException error which is almost certainly my fault putting something wrong in. However, now the Custom Builds page shows this error and I cannot make it go away. I have a local install, have killed and restarted, logged in and out, but still this error stays. I cannot try to enter another custom build because there is nothing on the page except this error. Does anyone kow how to get rid of this? Any help in getting around this error are appreciated. Jim

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fastq groomer
by arabidopsis 02 Nov '11

02 Nov '11

Hi all, Fastq groomer has Solexa or Illumina 1.3+ as an input quality format. I asked at the sequencing facility about their machine and output and they said their format was Illumina 1.8+ (the newest). I tried to convert my fastq file into Sanger by fastq groomer, using Illumina 1.3+ as an input option and got all reads with quality of around 10... Does it mean that Galaxy cannot be used on a dataset with 1.8+ encoding or something else was wrong? Thanks, Slon

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get data through FTP site
by Benoit HENNUY 02 Nov '11

02 Nov '11

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

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Re: [galaxy-user] Names for genes in RNA-Seq analysis
by Michael Gooch 02 Nov '11

02 Nov '11

Regarding the GTF files for cuffllinks, how do I obtain one for all human mRNA that actualy contains gene names rather than accession numbers. I went to the UCSC table browser but their files contain accession numbers that I dont know how to decode en-masse.

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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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