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

Re: [galaxy-user] using files produced by "Barcode Splitter"
by Jim Johnson 20 Jul '11

20 Jul '11

Jeremy, Usually, the users saved the files to their local machine by clicking on the links, and then uploaded them again to the galaxy server. It can be possible to copy the link location, and paste it into the upload tools URL textarea. Ideally, it would be nice for the tool developer to be able to include a link in the html that would "promote" the file to a dataset in the current history. JJ On 7/19/11 3:08 PM, Jeremy Coate wrote: > Thanks, Jim! > > I'll see if my limited Galaxy/bioinformatics skills can rise to the challenge of using your wrapper (I've never visited the "tool shed" before). > > Out of curiosity, how did people use the files generated by the barcode splitter without this? I'm assuming there was/is a way, but I'm not figuring it out. > > Jeremy > > > On Tue, Jul 19, 2011 at 11:26 AM, Jim Johnson <johns198(a)umn.edu <mailto:johns198@umn.edu>> wrote: > > I've had users make a similar request for the split files to appear in their history. I made my own wrapper to enable this behavior. It presents a list of barcodes from the barcode file input. Any barcodes the user selects will have the resulting files copied to the users history as new datasets. I uploaded my barcode splitter tool configs to the toolshed: http://toolshed.g2.bx.psu.edu/ as repository: barcode_splitter JJ Date: Mon, 18 Jul 2011 13:33:58 -0700 From: Jeremy Coate <jec73(a)cornell.edu> <mailto:jec73@cornell.edu> To: David K Crossman <dkcrossm(a)uab.edu> <mailto:dkcrossm@uab.edu> Cc: "galaxy-user(a)lists.bx.psu.edu" <mailto:galaxy-user@lists.bx.psu.edu> <galaxy-user(a)lists.bx.psu.edu> <mailto:galaxy-user@lists.bx.psu.edu> Subject: Re: [galaxy-user] using files produced by "Barcode Splitter" Message-ID: <CAA2BWd5uERaqEoUeQ97TfNhkwvHziq89wHVR-Oy04ov-K4ju6Q(a)mail.gmail.com> <mailto:CAA2BWd5uERaqEoUeQ97TfNhkwvHziq89wHVR-Oy04ov-K4ju6Q@mail.gmail.com> Content-Type: > text/plain; charset="iso-8859-1" Thanks David, I had considered this possibility but, curiously, the files don't show up in the FastQ Groomer pull-down menu either. The original (multiplexed) data file that I split using the Barcode Splitter is there (and, incidentally, I ran FastQ Groomer on that before doing the barcode split), but none of the 3 files resulting from the splitter show up. Any other thoughts? It seems like the new files just aren't landing in my history, though I can look at them by clicking their links from the Barcode Splitter output. Jeremy On Mon, Jul 18, 2011 at 12:01 PM, David K Crossman <dkcrossm(a)uab.edu> <mailto:dkcrossm@uab.edu> wrote: > >> Jeremy,**** ** ** The files need to be groomed using the FastQ Groomer so that they will end up in the fastqsanger state. Then your files will show up in the pull-down menus.**** ** ** David**** ** ** ** ** *From:* galaxy-user-bounces(a)lists.bx.psu.edu <mailto:galaxy-user-bounces@lists.bx.psu.edu> [mailto: galaxy-user-bounces(a)lists.bx.psu.edu <mailto:galaxy-user-bounces@lists.bx.psu.edu>] *On Behalf Of *Jeremy Coate *Sent:* Monday, July 18, 2011 1:44 PM *To:* galaxy-user(a)lists.bx.psu.edu <mailto:galaxy-user@lists.bx.psu.edu> >> >> *Subject:* [galaxy-user] using files produced by "Barcode Splitter"**** >> >> ** ** >> >> I used the "Barcode Splitter" tool to split multiplexed RNA-Seq libraries >> into separate files. I would now like to map the reads from each of these >> fastq files to a reference genome. However, the fastq files generated by >> Barcode Splitter don't appear in the "Fastq File" pull-down menus within the >> the BWA or Bowtie launch pages. I'm probably missing something obvious, but >> what is the trick for making these files available for the mapping tools? Do >> I need to import them into my history somehow?**** >> >> ** ** >> >> Thanks! >> Jeremy**** >> > > > > > > ___________________________________________________________ > 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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Re: [galaxy-user] using files produced by "Barcode Splitter"
by Jim Johnson 19 Jul '11

19 Jul '11

I've had users make a similar request for the split files to appear in their history. I made my own wrapper to enable this behavior. It presents a list of barcodes from the barcode file input. Any barcodes the user selects will have the resulting files copied to the users history as new datasets. I uploaded my barcode splitter tool configs to the toolshed: http://toolshed.g2.bx.psu.edu/ as repository: barcode_splitter JJ Date: Mon, 18 Jul 2011 13:33:58 -0700 From: Jeremy Coate <jec73(a)cornell.edu> To: David K Crossman <dkcrossm(a)uab.edu> Cc: "galaxy-user(a)lists.bx.psu.edu" <galaxy-user(a)lists.bx.psu.edu> Subject: Re: [galaxy-user] using files produced by "Barcode Splitter" Message-ID: <CAA2BWd5uERaqEoUeQ97TfNhkwvHziq89wHVR-Oy04ov-K4ju6Q(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Thanks David, I had considered this possibility but, curiously, the files don't show up in the FastQ Groomer pull-down menu either. The original (multiplexed) data file that I split using the Barcode Splitter is there (and, incidentally, I ran FastQ Groomer on that before doing the barcode split), but none of the 3 files resulting from the splitter show up. Any other thoughts? It seems like the new files just aren't landing in my history, though I can look at them by clicking their links from the Barcode Splitter output. Jeremy On Mon, Jul 18, 2011 at 12:01 PM, David K Crossman <dkcrossm(a)uab.edu> wrote: > Jeremy,**** > > ** ** > > The files need to be groomed using the FastQ Groomer so > that they will end up in the fastqsanger state. Then your files will show > up in the pull-down menus.**** > > ** ** > > David**** > > ** ** > > ** ** > > *From:*galaxy-user-bounces@lists.bx.psu.edu [mailto: > galaxy-user-bounces(a)lists.bx.psu.edu] *On Behalf Of *Jeremy Coate > *Sent:* Monday, July 18, 2011 1:44 PM > *To:*galaxy-user@lists.bx.psu.edu > *Subject:* [galaxy-user] using files produced by "Barcode Splitter"**** > > ** ** > > I used the "Barcode Splitter" tool to split multiplexed RNA-Seq libraries > into separate files. I would now like to map the reads from each of these > fastq files to a reference genome. However, the fastq files generated by > Barcode Splitter don't appear in the "Fastq File" pull-down menus within the > the BWA or Bowtie launch pages. I'm probably missing something obvious, but > what is the trick for making these files available for the mapping tools? Do > I need to import them into my history somehow?**** > > ** ** > > Thanks! > Jeremy**** >

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Re: [galaxy-user] Enis: [galaxy-bugs] Security Groups int the cloud
by Enis Afgan 19 Jul '11

19 Jul '11

Hi Luciano, Did you first create the galaxyWeb security group? Instructions are available on usegalaxy.org/cloud under Step 1. Enis > On 7/18/11 2:37 PM, Luciano Cosme wrote: > >> Hi, >> I am trying to run Galaxy in the cloud and I am following your >> screencast. I am having a problem when I need to choose the Security >> Groups, there is only the default showing up. I don't see galaxyWeb. I >> tried all AMI listed in your website and none worked. Then I proceed and >> launch it. I copy and paste the public DNS, but it is not working (even >> after 20 min). Is there anything that I might missing? >> >> Thank you. >> Luciano Cosme >> >> >>

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using files produced by "Barcode Splitter"
by Jeremy Coate 18 Jul '11

18 Jul '11

I used the "Barcode Splitter" tool to split multiplexed RNA-Seq libraries into separate files. I would now like to map the reads from each of these fastq files to a reference genome. However, the fastq files generated by Barcode Splitter don't appear in the "Fastq File" pull-down menus within the the BWA or Bowtie launch pages. I'm probably missing something obvious, but what is the trick for making these files available for the mapping tools? Do I need to import them into my history somehow? Thanks! Jeremy

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tailoring backend SGE submission requests to specific applications
by Joseph Hargitai 18 Jul '11

18 Jul '11

Hi, is there a best practices, to replace general SGE requests with requests specific to applications - did anyone actually build such request options to be part of the selectable items in the apps menus? best, joe

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Analyzing RNA-Seq replicates using Cuff(links/Compare/Diff)
by David K Crossman 14 Jul '11

14 Jul '11

Hello! I have 10 human RNA-Seq samples consisting of 3 groups (2 replicates per group). I have already run each of them through TopHat and Cufflinks on the Penn State Galaxy instance. I am now at a head-scratching moment. I want to use CuffCompare next (in the end I will want to run CuffDiff so that I can determine the gene/isoform expression between these 3 groups) but am unsure of the best way to do this. After reading several Galaxy posts, I've come across a couple of ideas: 1. Run CuffCompare on two Cufflinks output files. When that is finished take the CuffCompare output file and run it again in CuffCompare with the third Cufflinks output file sample. When this is finished, take that CuffCompare output file and run it again in CuffCompare with the fourth Cufllinks output file sample, etc... (I hope you catch my drift as to where this is going). In a nutshell I will be repeatedly merging Cufflinks outputs in CuffCompare. Then when all 10 have been put through CuffCompare, then I can run CuffDiff and set up 3 groups in CuffDiff with their appropriate BAM files from TopHat. 2. Add all 10 Cufflinks output files in CuffCompare using the "add new GTF input file" option. I chose step two because it looked the simplest and from the posts I read, it sounded like this was a fully functional option. I was also using a reference annotation file as well (that file has worked before in the past on non-replicate analyses). However, I came across an error: Error running cuffcompare. You are using Cufflinks v1.0.3, which is the most recent release. No fasta index found for ./input1. Rebuilding, please wait.. Error: sequence lines in a FASTA record must have the same length! cuffcompare v1.0.3 (2403) cuffcompare -o cc_output -r /galaxy/main_database/files/002/678/dataset_2678888.dat -R -s ./input1 ./input2 ./input3 ./input4 ./input5 ./input6 Any suggestions as to why this is happening? Am I trying something that shouldn't be attempted yet? Is there a better alternative to analyzing replicates? Any suggestions/ideas/workflows/you name it would be greatly appreciated!! Thanks, David

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generate pileup -v
by Matthew McCormack 14 Jul '11

14 Jul '11

Is choosing 'Print only lines containing indels' in the 'Whether or not to print only output lines containing indels' drop down for Generate pileup, the same as the -v option in SAMTools pileup ? Matthew 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.

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rna-seq CDS, splicing and TSS fails
by Richard Mark White 14 Jul '11

14 Jul '11

Hi all, So I am using cuffdiff to find significant differences between two samples (no replicates). The transcript and gene differential expression works and I get significant values. However, consistently, the TSS, CDS, and splicing differences return with "1 line" and no data. I have tried multiple different GTF transcriptome reference files - UCSC refflat, ensembl, but still no luck. Maybe I am missing something very basic - can anyone give me advice here? Richard

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cufflinks output in UCSC browser
by Aleks Schein 14 Jul '11

14 Jul '11

Hi all, I am doing cufflinks assembly of TopHat-aligned NGS reads with Refseq gene track as reference annotation. All works, but resulting gtf files cannot be displayed in UCSC browser. I use "display at UCSC main" link, but get a message:"Error 500: Internal Server Error". Has anyone experienced this problem recently? regards, Aleks

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Re: [galaxy-user] Workflow assistance
by Anton Nekrutenko 13 Jul '11

13 Jul '11

Kevin: Yes, for Illumina data BWA would be the best option from what is currently available at the main site. You can then identify variants with pileup and compare across the samples much as it is shown at http://usegalaxy.org/heteroplasmy. This should give you a rough idea on what to expect. However, piplines for proper (1000genomes-like) varinat calling that include realignment and recalibration steps are coming by the end of the Summer. Thanks! anton Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org On Jul 13, 2011, at 1:43 PM, Kevin Pawlik PhD wrote: > Hi, Anton: > > Diploid, 2x50 PE sequencing, rougly 5x coverage per sample. This is low coverage as a “first pass” - does that make a difference in the workflow strategy? Also, would BWA have been the better alignment option? > > Thank you, > > Kevin > > From: Anton Nekrutenko [mailto:anton@bx.psu.edu] > Sent: Wednesday, July 13, 2011 9:07 AM > To: Kevin Pawlik PhD > Cc: galaxy-user(a)lists.bx.psu.edu > Subject: Re: [galaxy-user] Workflow assistance > > Kevin: > > Is this a diploid or haploid organism? > > anton > galaxy team > > > Anton Nekrutenko > http://nekrut.bx.psu.edu > http://usegalaxy.org > > > > On Jul 12, 2011, at 11:38 PM, Kevin Pawlik PhD wrote: > > > After viewing tutorials and reading the information associated with various tools, I ask that you point me toward an appropriate workflow for the following: > > I sequenced (Illumina) 5 genomes of phenotype(+) samples and 1 genome of a phenotype(-) control. I uploaded fastqsanger files to Galaxy and performed Bowtie alignments. I want to find the allelic positions where the (+) genomes differ from the (-) genome. > > Many thanks, > > Kevin > > > > > ___________________________________________________________ > 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/ >

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