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

Lost history!
by Haiping Hao 23 Feb '11

23 Feb '11

I had two data file on galaxy and was grooming the data since Monday. I logged in to galaxy today and find my files are all gone. Any idea what happened? Thank you. Haiping -- ---------------------------------------------- JHMI Deep Sequencing and Microarray Core Facility at BRB - Your source for quality service on Microarray studies, NextGen Sequencing, and Data Analysis. http://www.microarray.jhmi.edu/ ---------------------------------------------- Haiping Hao Ph.D. Manager Johns Hopkins University Deep Sequencing and Microarray Core 733 N. Broadway, Rm 359 Baltimore, MD 21205 hhao(a)jhmi.edu Phone: 443-287-9056 Fax: 410-502-6666

2 1

Importing GTF into Galaxy
by Martin, David A. 23 Feb '11

23 Feb '11

Hi, I have been trying to get reference data from the ucsc browser into Galaxy, but when I try to get the rat genome in gtf format, I only get files halfway through chomosome 10. This happens with both of the available builds for the rat. I am guessing this is a problem with the UCSC files and not Galaxy. However, I was wondering if you could perhaps help with this issue. When I try to get just chromosome 10, the gtf file halts in the same place as it does when I try to get the whole genome, with this message at the bottom of the file: chr10 rn4_refGene start_codon 4293086 4293088 0.000000 + . gene_id "NM_001008876"; transcript_id "NM_001008876_dup1"; --------------------------------------------------------------------------- offsetToGenomic: need previous exon, but given index of 0 --------------------------------------------------------------------------- Any ideas? I have no problem importing the "KnownGenes" option in UCSC - would this file work well as a reference - what is the difference in the different files from UCSC(ie. "gene and gene prediction tracks" vs "mRNA and EST tracks" or "KnownGenes" vs "RefSeq)? I guess I could try to download each chromosome separately to avoid that line in chromosome 10 and then concatenate them. I tried downloading the rat GTF from Ensembl, but when I brought it into Galaxy, it wasn't formatted properly, and didn't have the NM_0001 accession numbers associated with it but rather some other type of label, so it looks like it might need some grooming before use with the NGS suite. Thank you for any suggestions, David Martin dmarti(a)lsuhsc.edu

2 1

Re: [galaxy-user] get wig file after tophat
by Jeremy Goecks 23 Feb '11

23 Feb '11

Ying, You can create a coverage file from a BAM file using this workflow: http://main.g2.bx.psu.edu/u/jeremy/w/create-coverage-dataset-from-bam-datas… While this doesn't generate a proper wiggle file, it can be a useful file for statistical analysis. I and others have suggested ways to visualize a BAM file with coverage data in mind: Trackster, IGV, and IGB. Thanks, J. On Feb 22, 2011, at 11:04 AM, Ying Zhang wrote: > Dear Jeremy: > > Thank you so much for helping me! > > Followed your instructions, I do get the pileup file, however, I am a little bit > confused about how you generate the wig file. So you mean to cut out the column > 1 and 4, and use the rest of them to generate the wig file or cut the columns 1 > and 4 and past it to another file to generate the wig file? The reason I am > asking is that it looks like column 1 is the information of chromosome, I am > not sure whether I should cut it out. Also I found out that the pileup file is > kind of big, so how you can cut the column 1 and 4? do you need to run a > command? I am basically not an expert in computer, do you know whether there is > an easy way to do this task in windows? THank u so much! > > Best > > Ying > > Quoting Jeremy Goecks <jeremy.goecks(a)emory.edu>: > >> Hi all, >> >> Ann is correct - Tophat does not produce .wig files when run anymore. However, it's fairly easy to use Galaxy to make a wiggle-like coverage file from a BAM file: >> >> (a) run the pileup tool on your BAM to create a pileup file; >> (b) cut columns 1 and 4 to get your coverage file. >> >> A final note: it's often difficult to visualize coverage files because they're so large. You might be better off visualizing the BAM file and using the coverage file for statistics. >> >> Best, >> J. >> >>> Hello, >>> >>> I think I know the answer (sort of) to this question. >>> >>> This may be because newer versions of tophat stopped running the "wiggles" >>> program, which is still part of the tophat distribution and is the program >>> that makes the "coverage.wig" file. >>> >>> A later version of tophat might bring this back, however - there's a note to >>> this effect in the tophat python code. >>> >>> So if you can run wiggles, you can make the "coverage.wig" file on your own. >>> >>> A student here at UNC Charlotte (Adam Baxter) made a few changes to the >>> "wiggles" source code that would allow you to use it with samtools to make a >>> "coverage.wig" file from the "accepted_hits.bam" file that TopHat creates. >>> >>> If you (or anyone else) would like a copy, please email Adam, who is cc'ed >>> on this email. >>> >>> We would be happy to help add it to Galaxy if this would be of interest to >>> you or other Galaxy users. >>> >>> If there is any way we can be of assistance, please let us know! >>> >>> Very best wishes, >>> >>> Ann Loraine >>> >>> >>> On 2/21/11 3:39 PM, "Ying Zhang" <ying.zhang.yz323(a)yale.edu> wrote: >>> >>>> Hi: >>>> >>>> I am using tophat in galaxy to analyze my paired-end RNA-seq data and find out >>>> that after the tophat analysis, we can not get the wig file from it anymore >>>> which is used to be able to. Do you have any idea of how to still be able to >>>> get the wig file after tophat analysis? Thanks a lot! >>>> >>>> Best >>>> >>>> Ying Zhang, M.D., Ph.D. >>>> Postdoctoral Associate >>>> Department of Genetics, >>>> Yale University School of Medicine >>>> 300 Cedar Street,S320 >>>> New Haven, CT 06519 >>>> Tel: (203)737-2616 >>>> Fax: (203)737-2286 >>>> _______________________________________________ >>>> The Galaxy User list should be used for the discussion >>>> of Galaxy analysis and other features on the public >>>> server at usegalaxy.org. 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/ >>> >>> -- >>> Ann Loraine >>> Associate Professor >>> Dept. of Bioinformatics and Genomics, UNCC >>> North Carolina Research Campus >>> 600 Laureate Way >>> Kannapolis, NC 28081 >>> 704-250-5750 >>> www.transvar.org >>> >>> >>> _______________________________________________ >>> The Galaxy User list should be used for the discussion >>> of Galaxy analysis and other features on the public >>> server at usegalaxy.org. 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/ >> > > > > Ying Zhang, M.D., Ph.D. > Postdoctoral Associate > Department of Genetics, > Yale University School of Medicine > 300 Cedar Street,S320 > New Haven, CT 06519 > Tel: (203)737-2616 > Fax: (203)737-2286

2 1

Fwd: normalizing for number of tags
by Jennifer Jackson 23 Feb '11

23 Feb '11

Hi Nadege, I am forwarding your question to galaxy-user(a)bx.psu.edu which is the best place to send data questions, so that the entire team can provide input. We will get back to you as soon as possible. Thanks! Jen Galaxy team ------- Hi Jen, I am completely new to the field of ChIP-seq and have, what may seem to many, a very trivial problem. Assuming that I have 2 datasets that I want to compare after normalizing each to their respective inputs, and assuming that these 2 datasets have very different number of reads to start with, how can I first normalize each dataset for number of reads in Galaxy? is it something that users do? Thanks for your precious help, best Nadege ________________________________________

1 0

Peep view for history elements broken on IE?
by Peter 22 Feb '11

22 Feb '11

Hi all, I've recently been testing Galaxy on Microsoft Internet Explorer, IE6 and now IE7. It seems that the "peep" view for history entries isn't supported. The history elements' names are not links, so clicking on them does not make them expand to show the info (e.g. number of sequences of file size, and the start of the data). This happens both on the public Galaxy instance at Penn State (http://usegalaxy.org) and our local Galaxy instance. Is this a known issue? Peter

3 13

fastx_clipper.xml and FASTQ Illumina 1.3+?
by Peter 22 Feb '11

22 Feb '11

Hi all, Should the fastx_clipper.xml allow Illumina 1.3+ FASTQ as well as Sanger and Solexa FASTQ (and FASTA)? i.e. replace this: <param format="fasta,fastqsolexa,fastqsanger" name="input" type="data" label="Library to clip" /> with this: <param format="fasta,fastqsolexa,fastqillumina,fastqsanger" name="input" type="data" label="Library to clip" /> Peter

2 1

Generating pileup for SNP analysis
by Christine Picard 22 Feb '11

22 Feb '11

I am a new user to Galaxy, and I was hoping someone might be able to help with this small problem. I am using Drosophila resequencing data downloaded from the SRA and trying to look for SNPs that differentiate the two strains. I've gotten as far as generating the pileup for each strain, but my column which has the consensus base is always an N. Can anyone help me out? thanks, Christine -- Christine J. Picard, Ph.D. Postdoctoral Research Associate Department of Entomology Texas A&M University TAMU 2475 College Station, TX 77843-2475 christine.picard(a)gmail.com

2 2

Re: [galaxy-user] get wig file after tophat
by David Matthews 22 Feb '11

22 Feb '11

HI, The option you need in IGV tools is "count". You set a window size and this gives you a tdf file from your sorted bam (or sam) file which is nice and quick to view on IGV. Best Wishes, David. __________________________________ Dr David A. Matthews Senior Lecturer in Virology Room E49 Department of Cellular and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol Bristol. BS8 1TD U.K. Tel. +44 117 3312058 Fax. +44 117 3312091 D.A.Matthews(a)bristol.ac.uk On 22 Feb 2011, at 15:52, Ying Zhang wrote: > Dear David: > > thank you very much for helping me! > > I have download the IGV and I do find the IGVtools, however, I am not sure which > tool I should use for generate a tdf file, the tile function will generate a tdf > file, but the input file format does not include bam or sam file, instead it > need wig file. But I have no wig file to put in. So I am wondering whether you > need to use other tool first. I really appreciate your help! Thank you very > much! > > Best > > Ying > > Quoting David Matthews <D.A.Matthews(a)bristol.ac.uk>: > >> Hi, >> >> You can get an equivalent visualisation from the IGV viewer by the Broad Institute - its under IGV tools and generates a tdf file from bam or sam files. This also gives a quick and easy way of looking at depth at any particular site and is very accessible. >> >> Cheers >> David >> >> >> On 21 Feb 2011, at 21:44, Jeremy Goecks wrote: >> >>> Hi all, >>> >>> Ann is correct - Tophat does not produce .wig files when run anymore. However, it's fairly easy to use Galaxy to make a wiggle-like coverage file from a BAM file: >>> >>> (a) run the pileup tool on your BAM to create a pileup file; >>> (b) cut columns 1 and 4 to get your coverage file. >>> >>> A final note: it's often difficult to visualize coverage files because they're so large. You might be better off visualizing the BAM file and using the coverage file for statistics. >>> >>> Best, >>> J. >>> >>>> Hello, >>>> >>>> I think I know the answer (sort of) to this question. >>>> >>>> This may be because newer versions of tophat stopped running the "wiggles" >>>> program, which is still part of the tophat distribution and is the program >>>> that makes the "coverage.wig" file. >>>> >>>> A later version of tophat might bring this back, however - there's a note to >>>> this effect in the tophat python code. >>>> >>>> So if you can run wiggles, you can make the "coverage.wig" file on your own. >>>> >>>> A student here at UNC Charlotte (Adam Baxter) made a few changes to the >>>> "wiggles" source code that would allow you to use it with samtools to make a >>>> "coverage.wig" file from the "accepted_hits.bam" file that TopHat creates. >>>> >>>> If you (or anyone else) would like a copy, please email Adam, who is cc'ed >>>> on this email. >>>> >>>> We would be happy to help add it to Galaxy if this would be of interest to >>>> you or other Galaxy users. >>>> >>>> If there is any way we can be of assistance, please let us know! >>>> >>>> Very best wishes, >>>> >>>> Ann Loraine >>>> >>>> >>>> On 2/21/11 3:39 PM, "Ying Zhang" <ying.zhang.yz323(a)yale.edu> wrote: >>>> >>>>> Hi: >>>>> >>>>> I am using tophat in galaxy to analyze my paired-end RNA-seq data and find out >>>>> that after the tophat analysis, we can not get the wig file from it anymore >>>>> which is used to be able to. Do you have any idea of how to still be able to >>>>> get the wig file after tophat analysis? Thanks a lot! >>>>> >>>>> Best >>>>> >>>>> Ying Zhang, M.D., Ph.D. >>>>> Postdoctoral Associate >>>>> Department of Genetics, >>>>> Yale University School of Medicine >>>>> 300 Cedar Street,S320 >>>>> New Haven, CT 06519 >>>>> Tel: (203)737-2616 >>>>> Fax: (203)737-2286 >>>>> _______________________________________________ >>>>> The Galaxy User list should be used for the discussion >>>>> of Galaxy analysis and other features on the public >>>>> server at usegalaxy.org. 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/ >>>> >>>> -- >>>> Ann Loraine >>>> Associate Professor >>>> Dept. of Bioinformatics and Genomics, UNCC >>>> North Carolina Research Campus >>>> 600 Laureate Way >>>> Kannapolis, NC 28081 >>>> 704-250-5750 >>>> www.transvar.org >>>> >>>> >>>> _______________________________________________ >>>> The Galaxy User list should be used for the discussion >>>> of Galaxy analysis and other features on the public >>>> server at usegalaxy.org. 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 Galaxy User list should be used for the discussion >>> of Galaxy analysis and other features on the public >>> server at usegalaxy.org. 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 Galaxy User list should be used for the discussion >> of Galaxy analysis and other features on the public >> server at usegalaxy.org. 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/ >> > > > > Ying Zhang, M.D., Ph.D. > Postdoctoral Associate > Department of Genetics, > Yale University School of Medicine > 300 Cedar Street,S320 > New Haven, CT 06519 > Tel: (203)737-2616 > Fax: (203)737-2286

3 2

Re: [galaxy-user] Generating pileup for SNP analysis
by Jennifer Jackson 22 Feb '11

22 Feb '11

Hello Christine, The data issue goes back to the initial grooming step. When using "Fastq Groomer", choose "Solexa" instead of "Illumina 1.3+" as the Input FASTQ quality score type. This preserves the correct quality score translation, which was the root of the problem in the derivative steps. Hopefully this helps when you do the re-run of the analysis, but please let us know if we can help more. I'll send you a link off-line to a history with some more specific information to your project, Thanks, Jen Galaxy team > On Wed, Feb 16, 2011 at 9:10 AM, Jennifer Jackson <jen(a)bx.psu.edu > <mailto:jen@bx.psu.edu>> wrote: > > Hi Christine, > > Would you like to share a link to your history? Use Options -> Share > or Publish and we can take a look at the input data (likely the > source of problem). > > Best, > > Jen > Galaxy team > > > On 2/11/11 7:20 AM, Christine Picard wrote: > > I am a new user to Galaxy, and I was hoping someone might be able to > help with this small problem. I am using Drosophila > resequencing data > downloaded from the SRA and trying to look for SNPs that > differentiate > the two strains. I've gotten as far as generating the pileup > for each > strain, but my column which has the consensus base is always an > N. Can > anyone help me out? > > thanks, Christine > > -- > Christine J. Picard, Ph.D. > Postdoctoral Research Associate > Department of Entomology > Texas A&M University > TAMU 2475 > College Station, TX > 77843-2475 > christine.picard(a)gmail.com <mailto:christine.picard@gmail.com> > <mailto:christine.picard@gmail.com > <mailto:christine.picard@gmail.com>> > > > > _______________________________________________ > 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>. 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 > > > > > -- > Christine J. Picard, Ph.D. > Postdoctoral Research Associate > Department of Entomology > Texas A&M University > TAMU 2475 > College Station, TX > 77843-2475 > christine.picard(a)gmail.com <mailto:christine.picard@gmail.com> > -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org

1 0

Group and hide steps in history/workflow
by Felix Hammer 22 Feb '11

22 Feb '11

Hi, it would be really nice if I could take a work flow and save it as a tool. This way one could easily build custom text-manipulation tools from already existing text tools. I already have a work flow that does a conversion job. But it has lots of of steps that make my histories quite messy when I apply it. Is there a way to condense the steps in the history view, so you can only see the name of a work flow and not all the separate steps? thx, Felix

2 4