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

BAM files
by Edward Dudley 20 Apr '11

20 Apr '11

Hi - I have a set of 454 reads that have been trimmed and converted to BAM format using Galaxy, and I can visualize the alignment with E. coli genomes using the UCSC browser. Problem is, I'd like to display the alignment in Artemis, but Artemis doesn't seem to want to read the .BAM file downloaded from Galaxy; I can import my genome sequence but when trying to import the BAM a blank window with "message" in the header keeps popping up. Anyone else tried to do this, and is there something about the Galaxy BAM files that Artemis doesn't like? Thanks. Ed

3 2

Re: [galaxy-user] downstream analysis of cuffdiff out put
by Jeremy Goecks 18 Apr '11

18 Apr '11

Vasu, Please reply to the mailing list as emails to individual Galaxy developers often get lost, and there are others on the list that might be able to help you or benefit from this discussion. Now, to your question: you're using the wrong GFF filtering tool, which is an easy mistake to make as there are many of them. You want to use Filter and Sort --> GFF --> Filter GTF data by attribute values list. Using this tool, I was able to filter dataset 11--a GTF file produced by Cuffcompare--using a Cuffdiff isoform expression file (dataset 10) on transcript_id. I've shared the modified history with you. Best, J. On Apr 18, 2011, at 3:29 PM, vasu punj wrote: > Hi Jeremy, > > I have been trying to use the tool mentioned in this message. > I have two samples comparison 6 and 5 and has run Cufflink/ > Cuffcompare/ Cuffdiff. I have filtred the files for c12 i.e for > significant analysis and file is 10 uploaded as B_A Cuffdiff isoform > expr filtered.txt > I uploaded the second file 11 > B_A_Homo_sapiens.GRCh37.60.clean.combined which is a combined GTF > file generated by cuffcompare. > > When I tried to run filter combined transcript file using: > Combined GTF as Cufflink assembled transcripts (11) and Cuffcompare > tracking file as Cuffdiff isoform exp filtered file using sample no > as 2, it return an empty file (12) > Than thinking that perhaps it may be tracking file which I may have > to use instead of combined GTF. > I used B-A combined tracking file in place of combined GTF file but > it will pop up only in Cuffcompare tracking file It may not be right > but I used File 13 as > tracking file with combined GTF as as assembled transcript still it > return empty out put > I have also shared history with you. > > Would you like to point me what is going on here? > Thanks. > > > Vasu > --- On Mon, 4/11/11, Jeremy Goecks <jeremy.goecks(a)emory.edu> wrote: > > From: Jeremy Goecks <jeremy.goecks(a)emory.edu> > Subject: Re: [galaxy-user] downstream analysis of cuffdiff out put > To: "shamsher jagat" <kanwarjag(a)gmail.com> > Cc: "galaxy-user" <galaxy-user(a)lists.bx.psu.edu> > Date: Monday, April 11, 2011, 9:04 AM > >> On Thu, Mar 10, 2011 at 7:55 AM, Jeremy Goecks <jeremy.goecks(a)emory.edu >> > wrote: >> Jagat, >> Just like any mRNA-seq experiment to achieve following objectives: >>> 1. Reconstruct all transcripts of a particular gene and >>> corresponding Cuffdiff significantly expressed transcripts as >>> called by cuffdiff. >>> 2. What are different isoforms >>> 3. Location of splicing >>> >>> From various output files which unique ID can be matched from one >>> file say Cuffdiff.expr (transcript/ isoform/Splicing) to other >>> file - transcript.gtf corresponding to each sample or combined >>> GTF file. >> I've got a script that does this for the cuffdiff isoform >> expression testing file and a GTF file; I'll wrap it up and add it >> to Galaxy in the next couple weeks. It would probably be useful to >> have similar scripts for the other expression testing files as >> well. Also, it would be nice to be able to take the FPKM values >> generated by Cuffdiff and attach them to their respective >> transcripts as attributes. > > Hello all, > > I've added a tool called 'Filter GTF file by attribute values list' > to the galaxy-central code repository. This tool is available on our > test server ( http://test.g2.bx.psu.edu/ ) at Filter and Sort --> > GFF --> Filter GTF data by attribute values list and will be > available on our main server in the next few weeks. > > As expected, this tool filters a GTF file based on a list of > attribute values--or filters using a tabular file where attribute > values are first column, as is the case for Cuffdiff output files. > Potential attributes that can be filtered on include transcript_id, > gene_id, tss_id, and p_id; conveniently, these are the IDs that > Cuffdiff uses in its output files. > > Here's an example workflow: > > (1) Run Cufflinks/compare/diff > (2) Filter Cufflinks isoform differential expression file for > transcripts that are differentially expressed; in other words, > filter for c12=='yes' > (2) Use 'Filter GTF data by attribute values list' to filter > Cuffcompare combined transcripts using the filtered file from step > (2) as the attribute values list and, voila, you have a GTF file of > the differentially expressed transcripts that you can view in your > favorite genome browser. > > Hope this helps; feedback is always welcome. > > Best, > J. > > -----Inline Attachment Follows----- > > ___________________________________________________________ > 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/

1 0

how to generate consensus sequence in galaxy
by vaibhav jain 18 Apr '11

18 Apr '11

Hi,I have some 14,000 genomic sequence of same length and i want to generate consensus sequence out if it. How can i do it in Galaxy ???Thanks in advance Vaibhav Jain Research Scholar @IGIB Delhi, INDIA

2 1

Map with Bowtie
by Sher, Falak 18 Apr '11

18 Apr '11

Hi Colleagues, I mapped illumina sequences using Bowtie on Galaxy server, I could not locate the information, like how many there were total reads and in what percentage they are mapped with mouse genome etc (samples were from mouse). Help and suggestions are greatly acknowledged, Thank you for attention, Falak

2 2

database on the cloud
by Randall, Thomas (NIH/NIEHS) [C] 18 Apr '11

18 Apr '11

I set up a galaxy instance on the cloud, but got the following error when trying to convert a bed file of hg18 coordinates to fasta sequence with the "Extract Genomic DNA" tool as a test of the functionality of this instance: No sequences are available for 'hg18', request them by reporting this error. Where did I go wrong? Likely I would get a similar error for other databases and indexes I might need and the instructions on the bitbucket site does not cover this (https://bitbucket.org/galaxy/galaxy-central/wiki/cloud) Otherwise this is a very nice setup. Thomas Randall, PhD Bioinformatics Scientist, Contractor National Institute of Environmental Health Sciences P.O. Box 12233, Research Triangle Park, NC 27709 randallta2(a)niehs.nih.gov<mailto:randallta2@niehs.nih.gov> 919-541-2271

3 2

unsubscribe
by Widmer, Giovanni F. 18 Apr '11

18 Apr '11

Hi, I have been trying to unsubscribe from this list as it jams up my inbox. I read that a confirmation will be send but that e-mail has never arrived. I there a way anyone can remove my e-mail address? Thanks.

5 5

Re: [galaxy-user] [Gmod-help] Missing tools in my configured galaxy
by Scott Cain 18 Apr '11

18 Apr '11

Hi Peter, I can't help you with that, so I'm going to forward this to the galaxy-user mailing list, galaxy-user(a)lists.bx.psu.edu, where presumably someone will know the answer. Scott On Mon, Apr 18, 2011 at 10:21 AM, Peter Tonge <peter_tonge_(a)hotmail.com> wrote: > > Hi, I have configured Galaxy on my desktop and it appears to be running fine. However, I suspect that I am missing tools from the galaxy-dist/tools. When I try to run the 'group' command from the join, subtract and group tab I get this error below: > > > > > And when I look in my computers directory (galaxy-dist/tools) for the py scripts there isn't a script for 'join, subtract and group'. This is also the case for Graph/Display data. Thus, when I try to run Graph/display data I get the same error. How can I rectify this? I configured the Galaxy suite yesterday, following the on-line Galaxy tutorial. Is it possible for somebody to forward the relevant py scripts for my to place in my galaxy-dist/tools directory. > > I look forward to hearing your advice, > Pete > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research

2 1

Normalization an dplotting of RPKM/FPKM after cufflink
by vasu punj 17 Apr '11

17 Apr '11

Hi, I want to include the following discussion in my message regarding use Bam files of Tophat to visualize reads either in IGV or Galaxy or other tools. I want to find out if I can plot RPKM/FPKM normalized values after running differential analysis in Cufflinks. On the seqanswer (http://seqanswers.com/forums/showthread.php?t=9947 ) there is a preliminary discussion about this how we can plot RPKM values to show the differential abundance in samples. Do we have any of such functionality in Galaxy? alternatively, I would like to have suggestions on the topic especially to normalize per million reads. Thanks. --- On Tue, 2/22/11, Jeremy Goecks <jeremy.goecks(a)emory.edu> wrote: From: Jeremy Goecks <jeremy.goecks(a)emory.edu> Subject: Re: [galaxy-user] get wig file after tophat To: "David Matthews" <D.A.Matthews(a)bristol.ac.uk> Cc: "Baxter, Adam" <Adam.Baxter(a)uncc.edu>, galaxy-user(a)bx.psu.edu Date: Tuesday, February 22, 2011, 11:30 AM All, For visualization, Galaxy now provides a built-in browser called Trackster. Trackster can visualize BAM files--as well as the junction file produced by Tophat and the GFF files produced by Cufflinks--and also provides coverage/summary information for all datatypes (see attached image). You can start using Trackster by going to the Visualization --> New Track Browser to set up a browser and add tracks. Alternatively, you can click on the Trackster icon in a dataset to visualize the dataset in a new or existing visualization (see attached image). Thanks, J. On Feb 22, 2011, at 11:54 AM, David Matthews wrote: 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 -----Inline Attachment Follows----- _______________________________________________ /

4 4

java client
by Reema Popley 15 Apr '11

15 Apr '11

Hi i have java client of my tools i need to integrate them in galaxy..so i basically need to convert those java client into xml.....but i m not sure whether java clients can be integrated in galaxy or not...please let me knw d same....Thank you

1 0

from Bowtie mapping to gene names
by Daniel Elleder 15 Apr '11

15 Apr '11

Hi, I have reads from Illumina paired-end run mapped against reference genome using Bowtie. Is there a Galaxy tool which would allow me to extract gene names from the mapped chromosomal regions? In this case I have cat genome, example of the output row is bellow. Thanks for anymhelp, Daniel HWUSI-EAS610_110227_00028:5:1:7767:999#0 99 chrE2 27900093 255 82M = 27900139 128 NACCTGTTATGTACTAAGAAGCTTATTCTCCCANNNNNNCTNNNNNNNNNCATATGTNGNGNNNNNNNNNNNNNNNNNNNAA ################################################################################## XA:i:2 MD:Z:0A17T14T0G0C0T0G0A2C0A0T0C0A0A0A0G0G7G1T1A0C0C0C0C0T0T0A0G0T0G0C0C0C0G0T0G0A0T2 NM:i:38 ------------------------------------------------ Daniel Elleder, Ph.D. Postdoctoral fellow Center for Infectious Disease Dynamics Pennsylvania State University 613 Mueller Laboratory University Park, PA 16802 tel: (814) 867-2122

5 15