January 2012 - galaxy-user - lists.galaxyproject.org

FASTQ joiner
by Matthew Herron 18 Jan '12

18 Jan '12

I am trying to join two groomed fastq files from a paired-end Illumina read using the fastq joiner tool. The drop-down menus correctly identify the groomed fastq files, but after cranking for a few minutes the tool produces empty output: "FASTQ joiner on data 5 and data 4 empty format: fastqsanger, database: ? Info: There were 3497909 known sequence reads not utilized. Joined 0 of 3497909 read pairs (0.00%)." The files have the same number of reads (3497909), reads have the same number of bases (102), and the joiner tool doesn't have any options (other than choosing the two files to join). Can anyone tell me what I'm doing wrong? Thanks, -- Matthew D. Herron, PhD Department of Zoology University of British Columbia X.princeps(a)gmail.com http://www.eebweb.arizona.edu/grads/mherron/

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Operate on genomic intervals: Join
by Stephen Eacker 18 Jan '12

18 Jan '12

Hello, I using operate on genomic intervals on some data and it always seems to ignore the strand information. Am I missing something or does "operate of genomic intervals" disregard strand information? Is there a tool that does the inner join function and takes into account strand information? thanks, Steve Stephen Eacker, Ph.D. Postdoctoral Fellow Dawson Lab Institute for Cell Engineering Johns Hopkins Medical Institute (443) 287-5605 seacker1(a)jhmi.edu

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cufflinks FPKM
by Li, Jilong (MU-Student) 18 Jan '12

18 Jan '12

Hi, I want to use cufflinks handle the results of Tophat. Cufflinks uses FPKM to normalize the expression data. I think FPKM is for pair-end reads. right? My reads are single-end. Is it right if I use FPKM? Thank you very much! Victor

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Deleted history
by Herve Rhinn 18 Jan '12

18 Jan '12

Hi, I have not been using Galaxy for a few months an it seems that a least one of my history was deleted. I assume it is because of inactivity for too long/exceeding the new quotas. Would there be by chance a a way to re-access it temporarily to be able to download some of that data or has it been totally erased? Thanks lot, Herve Rhinn

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BWA not recognize FASTQ query file
by Cai Shaojiang 18 Jan '12

18 Jan '12

Dear friends, We just installed a fresh galaxy on the server. Now when we try to run BWA following this tutorial: http://wiki.g2.bx.psu.edu/Admin/Training/Galaxy%20Admin%20Tutorial. It keeps telling that "FASTQ file: History does not include a dataset of the required format / build Must have Sanger-scaled quality values with ASCII offset 33" But we indeed have got the fastq file from http://lava.mathcs.emory.edu/outgoing/data/phiX174_reads.fastqsanger. And I also tried to upload a fastq file from my local disk. Still not working. So I am guessing maybe the default bwa wrapper is something wrong? Thanks. Yours: Cai -- Cai Shaojiang Department of Information Systems, School of Computing, National University of Singapore Tel: +65-65167355

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Galaxy Bowtie alignment stats report
by Eric Guo 18 Jan '12

18 Jan '12

Hello, Does anyone know how to get alignment stats from Bowtie on Galaxy? I would like to know what percentage of total reads from my dataset is aligned. I know if you run Bowtie using the command line, it gives you the report. However, I could not find percent alignment on Galaxy. Thanks in advance for the help! -Eric

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SNPEff - Reports Gain of Stop Codon as FRAME_SHIFT in some cases
by John David Osborne 18 Jan '12

18 Jan '12

Hi Pablo, Correct me if I am wrong, but I believe that SNPEff doesn't check the inserted sequence when computing the effect of an insertion? For instance an insertion of TTTA will be reported as a frameshift mutation. In the majority of cases this is fine, however if the current reading frame from the ORF annotation is the negative strand and the correct frame is selected the new codon will be: TAA T… The TAA is actually a stop codon, so the real effect of this insert should be insertion of a STOP CODON, not a frame shift in this instance. This is minor I know, but I though to report and make people aware. I am using version 2.02 of SNPEff, but I don't see this fix reported up to 2.04. -John

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Trouble getting tophat to run on built-in index genome
by Noa Sher 18 Jan '12

18 Jan '12

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Fixed parts inside workflows
by Saadeh, Heba 18 Jan '12

18 Jan '12

Dear All, I used to work with galaxy web site gladly, until I need to apply one workflow with (tens of join operations) on tens of datasets. so the problem is that if I need to run the workflow, each time I need to indicate the input datasets for each join operation and that is not interesting at all, and very time consuming. "although they are the same for each input file, in theory what I need to change is only the main input file, and leave the other files of the join operations the same, sound easy :)". I have read the comments for the "Workflows & Multiple datasets" post, on "how to run a workflow for multiple input files", and its now only working on galaxy-central, which I downloaded and used and it works fine and will solve one side of my problem the remaining will be with the fixed part inside the workflow. One last comment: the folder uploading functionality in galaxy-central is not working properly with me, the process continue until running the "uploading commands" but the files are all with 0 size, the same process on galaxy-dist works well... Much appreciated, heba --- Heba Saadeh Ph.D. Student Dept. of Medical and Molecular Genetics, Medicine School, King's College London, Guy's Hospital, 8th floor Tower Wing, London, SE1 9RT. Office: +44(0)20 7188 3715 ________________________________________ From: galaxy-user-bounces(a)lists.bx.psu.edu [galaxy-user-bounces(a)lists.bx.psu.edu] On Behalf Of Adhemar [azneto(a)gmail.com] Sent: 19 December 2011 18:35 To: Dannon Baker Cc: galaxy-user(a)lists.bx.psu.edu Subject: Re: [galaxy-user] Workflows & Multiple datasets I already tested and it's working like a charm. Thank you very much Dannon. -Adhemar 2011/12/19 Dannon Baker <dannonbaker(a)me.com<mailto:dannonbaker@me.com>> Ahh, I should have specified, that changeset is in the galaxy-central repository and has not been moved to galaxy-dist yet. I think we're testing a few more things, but this should happen in the near future, at which point you could simply update from galaxy-dist as usual, or you could pull directly from galaxy-central right now if you'd like. -Dannon On Dec 19, 2011, at 12:50 PM, Adhemar wrote: > Dannon, > Thanks for the immediate reply. > I just retrieved the latest code from the repository and it's not working > > $ hg summary > parent: 6298:b258de1e6cea tip > > > I also tried 'hg pull -u -r 6368:de03f821784b' but it says: > > pulling from https://bitbucket.org/galaxy/galaxy-dist > abort: unknown revision '6368:de03f821784b'! > > > How or when can I update to the release you mentioned? > Thanks, > -Adhemar > > > 2011/12/19 Dannon Baker <dannonbaker(a)me.com<mailto:dannonbaker@me.com>> > Adhemar, > > This was a bug that has been fixed as of changeset 6368:de03f821784b, which should be available on main.g2.bx.psu.edu<http://main.g2.bx.psu.edu> in the near future. If you're running a local instance, you'll find this resolved as soon as you update to that changeset or higher. > > Unfortunately, there isn't a fast way to copy datasets into a data library from multiple histories at once. I think you might find it faster to use the standard "Copy Datasets" functionality in the history Options menu to move everything you'd like into a single new history, and from there move it into a library. This Copy Datasets action allows you to select an individual history to copy from, instead of manually changing to the history first, so it should save you some time to do it that way. > > -Dannon > > > On Dec 19, 2011, at 12:12 PM, Adhemar wrote: > > > Hi, > > I was searching for how to run a workflow for multiple input files and I was very happy to find it's already implemented as mentioned here: http://wiki.g2.bx.psu.edu/News%20Briefs/2011_05_20 > > > > The problem is that it's not working for me. When I select two files, for example, it runs the workflow only in the first file. Even if I check 'Send results to a new history', it only creates a new history called 'test 1' and not the others. Is my instance somehow misconfigured or it's happening to others as well? > > > > I'm also looking for a way to add datasets to a library from different histories. Do I really need to open each history one by one and use 'Import datasets from your current library'? > > > > Thank you, > > Adhemar > > > > > > > > ___________________________________________________________ > > 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 > > > > To manage your subscriptions to this and other Galaxy lists, > > please use the interface at: > > > > http://lists.bx.psu.edu/ > >

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SAM tools pileup
by Patrick Kenneth Gonzales 18 Jan '12

18 Jan '12

Can we use the SAM tools pileup tool in Galaxy to get an accurate count of the coverage across the genome? I ask because I have run the pileup tool in Galaxy with bam files generated from tophat and noticed that the coverage reported in the pileup data was consistently lower then what I see in IGV. For example, I look at chr_1, coordinate 3515 and I see 10 reads mapped to that coordinate. I look in the pileup and it reads 1x coverage. I have not applied any filter to the pileup because all I want is a readout of the coverage at each NT including the number of variants that occur. My settings for generate pileup were: do not print mapping quality, print all lines, cap mapping quality to- 0, call consensus according to MAQ model- NO. Any suggestions? Is there a tool in Galaxy other than pileup that can do this? Thanks, Patrick

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