[galaxy-user] ftp not working
Hi, I'm still not able to use ftp - keeps saying connection refused either through the command line or through cyberduck - is anyone else seeing this? 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.matth...@bristol.ac.uk ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-user] Tophat error
Hi, JUst running a TopHat job which returned the following error: Executing: /gpfs/cluster/isys/galaxy/Software/bin/bowtie-inspect /local/tmp5Ywx45/dataset_942 ./tophat_out/tmp/dataset_942.fa [Tue Mar 13 12:45:08 2012] Checking for Bowtie Bowtie version: 0.12.7.0 [Tue Mar 13 12:45:08 2012] Checking for Samtools Samtools Version: 0.1.18 [Tue Mar 13 12:45:08 2012] Generating SAM header for /local/tmp5Ywx45/dataset_942 format: fastq quality scale: phred33 (default) [Tue Mar 13 12:45:21 2012] Preparing reads left reads: min. length=56, count=29523921 right reads: min. length=56, count=29543412 [Tue Mar 13 13:07:54 2012] Mapping left_kept_reads against dataset_942 with Bowtie [Tue Mar 13 13:45:26 2012] Processing bowtie hits [Tue Mar 13 14:11:28 2012] Mapping left_kept_reads_seg1 against dataset_942 with Bowtie (1/2) [Tue Mar 13 14:43:27 2012] Mapping left_kept_reads_seg2 against dataset_942 with Bowtie (2/2) [Tue Mar 13 14:57:50 2012] Mapping right_kept_reads against dataset_942 with Bowtie [Tue Mar 13 15:37:46 2012] Processing bowtie hits [Tue Mar 13 16:04:28 2012] Mapping right_kept_reads_seg1 against dataset_942 with Bowtie (1/2) [Tue Mar 13 16:37:18 2012] Mapping right_kept_reads_seg2 against dataset_942 with Bowtie (2/2) [Tue Mar 13 16:50:40 2012] Searching for junctions via segment mapping Traceback (most recent call last): File /gpfs/cluster/isys/galaxy/Software/bin/tophat, line 3063, in module sys.exit(main()) File /gpfs/cluster/isys/galaxy/Software/bin/tophat, line 3029, in main user_supplied_deletions) File /gpfs/cluster/isys/galaxy/Software/bin/tophat, line 2681, in spliced_alignment [maps[initial_reads[left_reads]].unspliced_bwt, maps[initial_reads[left_reads]].seg_maps[-1]], TypeError: list indices must be integers, not str Does anyone know what this kind of error is? 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.matth...@bristol.ac.uk ___ 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/
[galaxy-user] Tophat error
Hi, JUst running a TopHat job which returned the following error: Executing: /gpfs/cluster/isys/galaxy/Software/bin/bowtie-inspect /local/tmp5Ywx45/dataset_942 ./tophat_out/tmp/dataset_942.fa [Tue Mar 13 12:45:08 2012] Checking for Bowtie Bowtie version: 0.12.7.0 [Tue Mar 13 12:45:08 2012] Checking for Samtools Samtools Version: 0.1.18 [Tue Mar 13 12:45:08 2012] Generating SAM header for /local/tmp5Ywx45/dataset_942 format: fastq quality scale: phred33 (default) [Tue Mar 13 12:45:21 2012] Preparing reads left reads: min. length=56, count=29523921 right reads: min. length=56, count=29543412 [Tue Mar 13 13:07:54 2012] Mapping left_kept_reads against dataset_942 with Bowtie [Tue Mar 13 13:45:26 2012] Processing bowtie hits [Tue Mar 13 14:11:28 2012] Mapping left_kept_reads_seg1 against dataset_942 with Bowtie (1/2) [Tue Mar 13 14:43:27 2012] Mapping left_kept_reads_seg2 against dataset_942 with Bowtie (2/2) [Tue Mar 13 14:57:50 2012] Mapping right_kept_reads against dataset_942 with Bowtie [Tue Mar 13 15:37:46 2012] Processing bowtie hits [Tue Mar 13 16:04:28 2012] Mapping right_kept_reads_seg1 against dataset_942 with Bowtie (1/2) [Tue Mar 13 16:37:18 2012] Mapping right_kept_reads_seg2 against dataset_942 with Bowtie (2/2) [Tue Mar 13 16:50:40 2012] Searching for junctions via segment mapping Traceback (most recent call last): File /gpfs/cluster/isys/galaxy/Software/bin/tophat, line 3063, in module sys.exit(main()) File /gpfs/cluster/isys/galaxy/Software/bin/tophat, line 3029, in main user_supplied_deletions) File /gpfs/cluster/isys/galaxy/Software/bin/tophat, line 2681, in spliced_alignment [maps[initial_reads[left_reads]].unspliced_bwt, maps[initial_reads[left_reads]].seg_maps[-1]], TypeError: list indices must be integers, not str Does anyone know what this kind of error is? 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.matth...@bristol.ac.uk ___ 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/
[galaxy-user] Make a vcf file
Hi, This may be a dense question, but how do we generate a vcf file from the public version of Galaxy? Am I missing something obvious? 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.matth...@bristol.ac.uk ___ 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/
[galaxy-user] BLAST+ on the test site
Hi, I;m wanting to run BLASTp on the test site to compare it to some test runs here on our local copy but the tool does not run saying Index file named 'blastdb_p.loc' is required by tool but not available. Is this me doing something wrong or is it something missing at the test site? 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.matth...@bristol.ac.uk ___ 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/
Re: [galaxy-user] selecting reads at random from fastq file
Hi, This may be a bit dumb or missing the point but just selecting the first 5 million is kind of random isn't it? I mean where the reads map and what they are from is not known to you and they were not collected by the sequencer in a manner that is influenced by the nature of the sample? 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.matth...@bristol.ac.uk On 9 Nov 2011, at 09:44, Hans-Rudolf Hotz wrote: Hi Paul, Hi Peter You might also wanna look at the 'FastqSampler' function in the Bioconductor 'ShortRead' package http://bioconductor.org/packages/release/bioc/html/ShortRead.html We are working (as part of our NGS pipeline redesign) on adding more Bioconductor functionalities to Galaxy. Unfortunately, it is very low on my pile of stuff to do, so it will take a while till it appears in the 'Tool Shed'. Regards, Hans On 11/08/2011 11:45 PM, Peter Cock wrote: On Tue, Nov 8, 2011 at 10:26 PM, Austin Paulausti...@usc.edu wrote: Hi Peter, Thanks for the suggestion. For example, I have a fastq file with 50 million reads and I want to randomly select 5 million of them. It seems biopython would very easily select a single or a handful of reads with the Bio.SeqIO.index() function. Would it also be able to do the job I am interested in? Austin I think so, but you'd have to use Bio.SeqIO.index_db() which stores the index in an SQLite dictionary rather than in memory which isn't really viable here (unless you have a 64bit big memory machine?). I don't think I've tried it with quite that many reads though... Alternatively, if I understood her correctly, Jennifer pointed out you can do this in Galaxy but it will take a lot of IO: 1. Convert FASTQ to tabular (4 lines per record - 1 line per record) 2. Randomly select lines (each line is now a record so safe) 3. Convert tabular back to FASTQ It should work though, and requires no additional programming. Peter ___ 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/ ___ 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/ ___ 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/
Re: [galaxy-user] SNPeff tool?
Hi, I've had a few email chats with the author of snpEff and the fly in the ointment from my perspective is getting the vcf files it needs through Galaxy. As I understand it there is no way currently of getting the BAM/SAM files into the right input format so snpEff can use it within a Galaxy setup. So, whatever you do you'll still need one or two command line steps. We have a copy of snpEff here at Bristol on our Galaxy and when we did that we then realised there was no Galaxy method (that we could think of) for getting the input file ready for snpEFF to use. This is a pity as its actually a very nice piece of software with a nice professional looking output. 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.matth...@bristol.ac.uk On 8 Nov 2011, at 13:55, Dannon Baker wrote: Hi Laura, While the SNPeff developers have made Galaxy wrappers available, this is not a tool we currently have installed for use on the Galaxy server at main.g2.bx.psu.edu. Off the top of my head, I don't know of any other public Galaxy servers that offer this tool, but if you have access to a local or cloud galaxy server you could use the provided wrapper to install the tool for use there. Thanks! -Dannon On Nov 8, 2011, at 6:40 AM, Laura Elizabeth Spoor wrote: Hi, I use the Galaxy server and was wondering how to use SNPeff tool? I have seen that it can be integrating with Galaxy on their website (http://snpeff.sourceforge.net/images/snpEff_galaxy.png) but cannot see it on the server? Is it something that can be run on the server? Best Wishes, Laura -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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/ ___ 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/ ___ 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/
Re: [galaxy-user] SNPeff tool?
Hi, Yes, I see that you can generate the VCF files that way but there is no seamless way of doing it entirely from within galaxy - i.e. you need to come out of galaxy at some point (or am I missing something?). 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.matth...@bristol.ac.uk On 8 Nov 2011, at 14:39, Chorny, Ilya wrote: I got it working just fine on my local server. Could you expand on your vcf issue? I generate the vcf using gatk. Sent from my iPhone On Nov 8, 2011, at 6:36 AM, David Matthews d.a.matth...@bristol.ac.ukmailto:d.a.matth...@bristol.ac.uk wrote: Hi, I've had a few email chats with the author of snpEff and the fly in the ointment from my perspective is getting the vcf files it needs through Galaxy. As I understand it there is no way currently of getting the BAM/SAM files into the right input format so snpEff can use it within a Galaxy setup. So, whatever you do you'll still need one or two command line steps. We have a copy of snpEff here at Bristol on our Galaxy and when we did that we then realised there was no Galaxy method (that we could think of) for getting the input file ready for snpEFF to use. This is a pity as its actually a very nice piece of software with a nice professional looking output. 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.matth...@bristol.ac.ukmailto:d.a.matth...@bristol.ac.uk On 8 Nov 2011, at 13:55, Dannon Baker wrote: Hi Laura, While the SNPeff developers have made Galaxy wrappers available, this is not a tool we currently have installed for use on the Galaxy server at main.g2.bx.psu.edu. Off the top of my head, I don't know of any other public Galaxy servers that offer this tool, but if you have access to a local or cloud galaxy server you could use the provided wrapper to install the tool for use there. Thanks! -Dannon On Nov 8, 2011, at 6:40 AM, Laura Elizabeth Spoor wrote: Hi, I use the Galaxy server and was wondering how to use SNPeff tool? I have seen that it can be integrating with Galaxy on their website (http://snpeff.sourceforge.net/images/snpEff_galaxy.png) but cannot see it on the server? Is it something that can be run on the server? Best Wishes, Laura -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.orghttp://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/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.orghttp://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/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.orghttp://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/ ___ 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
[galaxy-user] Downloading large files from galaxy
Hi, I seem to be having problems downloading large files from galaxy - the request times out at about 1GB and I'm downloading 2-3GB. Am I doing something wrong? David ___ 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/
Re: [galaxy-user] miRNA NGS data processing
Hi, Tophat may still be an option for you. You can filter out spliced reads by filtering column 6 (the CIGAR column) for reads that only map directly (i.e. c6=='56M' if you have a 56bp paired end read). But I agree with Jen that most likely it is a sort problem. 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.matth...@bristol.ac.uk On 9 Aug 2011, at 07:27, yao chen wrote: Hi Mete, I am not sure it is the sort problem. I find cufflinks in galaxy is unstable. I have bam files from Tophat which I can run cufflinks a few days agao. But these days when I run cufflinks with these bam files, the error shows. Strangely, it can work some time. I don't know the reason. ChenYao 2011/8/9 Jennifer Jackson j...@bx.psu.edu Hi Mete, This FAQ has a workflow for sorting a Bowtie (or any) SAM file for Cufflinks: http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq#faq2 Thanks! Jen Galaxy team On 8/4/11 10:27 AM, Mete Civelek wrote: Hi, I'm trying to get read counts or FPKM values for my miRNA NGS data on Galaxy. I have aligned the reads using Bowtie, but it appears that Cufflinks gives an error when run on the Bowtie alignments (This might have something to do with Bowtie's BAM file not being sorted). I know that Tophat alignments work well with Cufflinks, but I'm not sure if it would be possible to use Tophat for my data since miRNA don't have splice junctions. I've tried without success to parameterize Tophat to completely avoid assigning splice junctions (by setting the max intron length to 1). Is there a way I can get the Bowtie alignment to work with Cufflinks on Galaxy? Or perhaps there's a way I can parametrize Tophat as to get no splice junctions? Thanks, Mete IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer. ___ 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/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/ ___ 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/ ___ 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/
Re: [galaxy-user] generating a new fasta from a pileup
Hi John, That would be totally fantastic - many thanks! 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.matth...@bristol.ac.uk On 30 Jul 2011, at 16:35, John Nash wrote: I have some code which can do most of the requested things. Let me figure out how to galaxy around it, and I'll submit it. John Sent from my mobile device On 2011-07-30, at 12:47 AM, Jennifer Jackson j...@bx.psu.edu wrote: Hello David, Generating a consensus fasta sequence from a BAM or Pile-up file is not yet possible in Galaxy. To date, the Tool Shed also does not have a wrapped/novel tool for this function either. If you or another user were to create such a wrapped tool, it would be most welcome. As would a tool that would replace the corresponding region of the reference genome with the variant fasta sequence to create a novel reference for alignments. Both great ideas that have been discussed a few times on the list and here among our team. If you wanted to open a bitbucket ticket, that would be one way to share exactly what you had in mind and give you a ticket to watch for if/when tools like this are added. Or, I can open one (or possibly two, one for each function) for you, just let me know. https://bitbucket.org/galaxy/galaxy-central/issues?status=newstatus=open Thanks for the great feedback, sorry there wasn't a solution (yet!), Best, Jen Galaxy team On 7/22/11 12:56 PM, David Matthews wrote: Hi On a separate issue, I have been having trouble generating a corrected fasta file based on a pileup. I have a dataset that is a resequenced genome and I want to correct the fasta file based on the consensus and then re run the alignments to see how it affects things. However, I cannot for the life of me figure out how to do it in Galaxy. Any help appreciated! David ___ 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/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/ ___ 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/ ___ 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/
Re: [galaxy-user] calculating percent coverage over the target genome
Hi Jen, Many thanks for this, on a related subject do you know of a way to correct a FASTA file on the basis of a pileup (or even just on the BAM file)? 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.matth...@bristol.ac.uk On 25 Jul 2011, at 17:52, Jennifer Jackson wrote: Hello David, To calculate coverage, please see the tool Regional Variation - Feature coverage. Query and target must both be in Interval/BED format. Query data in Interval/BED format is possible in most of the dataflow paths through the tools and from external sources. The reference genome file will likely need to be imported and formatted. This is simple example history where I pulled the chromInfo file from UCSC and formatted, extracted a subset of genes in BED format, and ran the Feature Coverage tool (both directions, see datasets 8 and 9). http://main.g2.bx.psu.edu/u/jen-bx-galaxy-edu/h/galaxy-user-calculating-percent-coverage-over-the-target-genome-7-22 Hopefully this helps, Jen Galaxy team On 7/22/11 12:32 PM, David Matthews wrote: Hi Does anyone know how to calculate how much of a genome was covered by an alignment irrespective of the depth at each base? Cheers David ___ 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/ ___ 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/
[galaxy-user] calculating percent coverage over the target genome
Hi Does anyone know how to calculate how much of a genome was covered by an alignment irrespective of the depth at each base? Cheers David ___ 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/
[galaxy-user] Looking for new transcripts with cufflinks
Hi, I am working with HeLa cells and want to know how to get cufflinks etc. to highlight if a region of the genome is being transcribed that is not in the ensembl gtf. I know that cufflinks highlights with class code j regions that do not match a known gene and therefore may be novel but most of these arise from transcription on or near known genes. Does anyone know how to look for transcription that is clearly distinct from known genes? This is a wild goose chase but worth a peek just in case... 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.matth...@bristol.ac.uk ___ 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/
Re: [galaxy-user] Looking for new transcripts with cufflinks
Of course - Doh! Many thanks!! On 4 Jul 2011, at 18:47, Oliver, Gavin wrote: u represents unknown intergenic transcripts. -Original Message- From: galaxy-user-boun...@lists.bx.psu.edu on behalf of David Matthews Sent: Mon 04/07/2011 17:48 To: galaxy-user@lists.bx.psu.edu Subject: [galaxy-user] Looking for new transcripts with cufflinks Hi, I am working with HeLa cells and want to know how to get cufflinks etc. to highlight if a region of the genome is being transcribed that is not in the ensembl gtf. I know that cufflinks highlights with class code j regions that do not match a known gene and therefore may be novel but most of these arise from transcription on or near known genes. Does anyone know how to look for transcription that is clearly distinct from known genes? This is a wild goose chase but worth a peek just in case... 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.matth...@bristol.ac.uk The contents of this message and any attachments to it are confidential and may be legally privileged. If you have received this message in error, you should delete it from your system immediately and advise the sender. Almac Group (UK) Limited, registered no. NI061368. Almac Sciences Limited, registered no. NI041550. Almac Discovery Limited, registered no. NI046249. Almac Pharma Services Limited, registered no. NI045055. Almac Clinical Services Limited, registered no. NI041905. Almac Clinical Technologies Limited, registered no. NI061202. Almac Diagnostics Limited, registered no. NI043067. All preceding companies are registered in Northern Ireland with a registered office address of Almac House, 20 Seagoe Industrial Estate, Craigavon, BT63 5QD, UK. Almac Sciences (Scotland) Limited, registered in Scotland no. SC154034. Almac Clinical Services LLC, Almac Clinical Technologies LLC and Almac Diagnostics LLC are Delaware limited liability companies and Almac Group Incorporated is a Delaware Corporation. More information on the Almac Group can be found on the Almac website: www.almacgroup.com ___ 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/
Re: [galaxy-user] Cufflinks advice
Hi, As a first guess I would say that your chromosome names do not match somewhere along the line. If you look at your sam file and the fasta of the genome you are working with (and the gtf file as well if you are using it) you may find, for example, one refers to chromosome 1 as chr1 whilst the other refers to chromosome 1 as 1 or even Chr1 or some other way of referring to the chromosome - any of these mismatches can cause you to get an empty output. If you are using a built in index it may be you need to change your chromosome names from 1 to chr1 for example. Amazingly, the names of human chromosomes are apparently not yet standardised across all databases for the human genome (and I presume this may be the case for other genomes as well). 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.matth...@bristol.ac.uk On 15 Jun 2011, at 02:22, Michael Gooch wrote: I attempted to run cufflinks on some RNA sequencing data. It seemed to complete without any errors, but the output files were empty. I am trying to figure out if I did something wrong or whether my data needs some additional processing before cufflinks will be able to use it. (Or whether the data is unsuitable for cufflinks.) The data is paired end reads. M. Gooch ___ 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/ ___ 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/
[galaxy-user] Converting transcriptomes to proteomes
Dear Galaxy users, I am trying to modify the human proteome based on my transcriptomeics data. In short I want to use my transcriptomics data to identify snps and from that identify coding changes that result from the snps. Ultimately I'd like to create a customised canonical proteome based on my transcriptomic data. Does anyone know how this might be done in Galaxy? I have started by running a pileup and so on but I am not a human geneticist (I am a virologist) so I may be making some fundamental errors!! Any help is gratefully received! 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.matth...@bristol.ac.uk ___ 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/
Re: [galaxy-user] Aligning against Multiple Reference Sequences
Hi John, Probably the simplest thing for you to do would be to concatenate the two genomes one after the other using the concatenate tool under text manipulation. This will generate a new organism with apparently two chromosomes one from bacteria A and one from bacteria B. When you run tophat or bowtie the sam file will indicate which chromosome (i.e. which bacteria) it assigned the read to. Hope this helps. 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.matth...@bristol.ac.uk On 9 Jun 2011, at 15:18, John David Osborne wrote: Are there any tools in Galaxy to align short reads against multiple reference sequences? I have a dozen microbial genomes sequenced for which there are 2 reference genomes already sequenced. We have tried aligning each of these individually against either of the reference genomes - some align better against the first reference genome, some align better against the second reference genome. Ideally though I would like to be able to align against both at the same time. Is this possible? I have found a tool called GenomeMapper and hints of 2 other tools in development that do something like this, but nothing for Galaxy yet. How do others proceed with this type of problem? Workflows appreciated! :) -John ___ 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/ ___ 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/
Re: [galaxy-user] RNA seq analysis
Hi, I have done exactly the same kind of thing for adenovirus so I can help with it. In answer to question 1 you do not need to index it will be done for you when tophat is called. Secondly you should leave the 40 multihits as it is and post analysis filter out the multihits - this will allow you to determine if you do have a multihit problem or not and if so whether it is a big problem and where it is on the genome. I have a workflow on Galaxy which you can use called Bristol workflow to get sorted unique proper pair mapped reads. If you plug in your sam file it should give you files listing only unique hits and those which map more than once. This workflow assumes you have paired end data but it can be modified to work with single end reads as well. Hope this helps. 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.matth...@bristol.ac.uk On 6 May 2011, at 17:09, puvan...@umn.edu wrote: Hi I have a couple of questions regarding RNA seq analysis. My questions are 1.I need to use a viral genome (very small, ~2kb ) as a reference genome and it is not available in Galaxy. I guess I can use this data from my history. I have a fasta file but I am not sure whether I have to do some kind of indexing or not. 2. In Tophat, default for maximum number of alignments to be allowed is 40. What my understanding is a single read can be aligned maximum 40 different places. I am wondering why this is 40. Is there any specific reason? If I need unique mapping, I have to use 1 instead of 40. Am I correct? Thanks SP ___ 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/ ___ 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/
[galaxy-user] SNPs, Indels and so on in virus genomes
Hi, I recently sent out an email asking if anyone knew much about analysis of SNPs etc and how to visualise them. I got some very useful answers and planned to return to the problem when I got a better chance to work on this in some depth. I now have the time but, like an idiot, I've accidentally deleted those email replies! So can I please ask again, does anyone have experience of SNP analysis and, especially, visualisation that can hold my hand whilst I work this out (apologies to the ones who replied last time but can you get in touch again !)? 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.matth...@bristol.ac.uk ___ 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/
Re: [galaxy-user] Around Pittsburgh on April 6? Attend the Intro to Galaxy Sessions @ Pitt
I would be very keen to see this as a webcast or similar - I'd even stay up late to watch it! On 31 Mar 2011, at 20:19, Dave Clements wrote: Hello all, Dan Blankenberg will be giving two workshops on Galaxy at the University of Pittsburgh on April 6. The presentations are open to the public. See below for details and please contact Dan, or Carrie Iwema at Pitt, if you have any questions. Thanks, Dave C. Intro to Galaxy http://galaxy.psu.edu/ Dan Blankenberg, PhD Center for Comparative Genomics Bioinformatics Penn State University Galaxy allows you to do analyses you cannot do anywhere else without the need to install or download anything. You can analyze multiple alignments, compare genomic annotations, profile metagenomic samples more... Wednesday 6th April 10 am – 12 pmIntro to Galaxy (general interest) 2 pm - 4 pmWorking w/NGS Data (advanced users) University of Pittsburgh Falk Library Conference Room B You are welcome to bring your laptop. Carrie L. Iwema, PhD, MLS Information Specialist in Molecular Biology Health Sciences Library System University of Pittsburgh 200 Scaife Hall 3550 Terrace St Pittsburgh, PA 15261 412-383-6887 412-648-8819 (fax) iw...@pitt.edu www.hsls.pitt.edu/molbio -- http://galaxy.psu.edu/gcc2011/ http://getgalaxy.org http://usegalaxy.org/ ___ 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/ ___ 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/
Re: [galaxy-user] Pseudo Autosomal regions in Chrs X and Y
Fantastic, many thanks! 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.matth...@bristol.ac.uk On 29 Mar 2011, at 00:19, Jennifer Jackson wrote: Hi David, The PAR regions are documented at UCSC on the hg19 genome gateway page (and for some other recent genomes). Start at the main page, click into Genomes, select hg19, then scroll down to credits: http://genome.ucsc.edu/ quote: The Y chromosome in this assembly contains two pseudoautosomal regions (PARs) that were taken from the corresponding regions in the X chromosome and are exact duplicates: chrY:10001-2649520 and chrY:59034050-59363566 chrX:60001-2699520 and chrX:154931044-155260560 Hopefully this helps! Jen On 3/28/11 2:04 PM, David Matthews wrote: Hi, Again, thanks for the feedback. I made my own female hg19 by deleting chrY from my copy of hg19 so thats OK. It still leaves the problem of how to analyse male transcriptomes since maps to PAR1 and 2 genes get reported as multimap reads which can end up being filtered out depending on how you analyse your transcriptome. If I knew with certainty where PAR1 and 2 are on chrY of hg19 I was planning to replace the nucleotides with N's on chrY so that they would no longer show up as a multimap problem - do you (or anyone else) happen to know the co-ordinates on hg19? Cheers David On 23 Mar 2011, at 14:19, Jennifer Jackson wrote: Hi David, Right now we don't have anything built-in to filter out this type of duplication automatically. As a potential option, did you know that we offer a Canonical Female build for certain genomes? This may help with some of the duplication issues, if the loss of novel Y is OK for your project. Please see: https://bitbucket.org/galaxy/galaxy-central/wiki/GenomeData Thanks for bringing up a good point! Best, Jen On 3/10/11 8:44 AM, David Matthews wrote: Hi All again, A separate point about the analysis of cufflinks data is the subject of the Pseudo Autosomal Regions in X and Y - this will make a mess of gene expression analysis in some cases especially because tophat will assign a read to both places which therefore makes it a multihit read (which you might then filter out) or it may double the true levels of reported expression. Anyone had experience/thoughts on this? 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.matth...@bristol.ac.ukmailto:d.a.matth...@bristol.ac.uk ___ 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 -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org ___ 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/
Re: [galaxy-user] A genbank to gtf converter
Hi Jen, Many thanks for the reply. Sadly my programming is not up to anything like a gbk to gtf converter! The main reason I want one is that as a virologist this would be very useful since many viruses do not have a gtf file but do have genbank submissions. I know of a site that has some viruses listed together with GFF files but alas I cannot find a GFF to GTF converter - nightmare!! I'll keep looking for one and if I find it I'll let you know. Cheers David On 23 Mar 2011, at 18:02, Jennifer Jackson wrote: Hello David, This is a great idea that the team has been considering adding, but nothing immediate is planned. There are some external teams that are working on outside development, and this is on their list, to. If interested in what that project is doing, please see this thread: http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-March/004692.html For now, if the data resides in a track at UCSC (many are, especially for vertebrate genomes and it is updated daily), using the Table browser can allow you to export the data in GTF and push to Galaxy with the Get Data tool. Since some of the data can be large, using BX Main (our local UCSC mirror) may be the best source. To do this, navigate to the target genome and track (RefSeq under Gene Predictions, others under Mrna EST), and choose output format GTF - gene transfer format. Please note that the gene_id attribute in the 9th field will not be populated with the gene name (will be same as transcript_id). This is just how UCSC does it right now (on their list to get the full GTF output set up in the TB, as far as we know). But, to get that info now, go back in and reexport the same table data again as all fields from selected table into Galaxy and the gene name will be in the data field named name2. The text manipulation tools can help to format the data. A workflow would be a good option once you have the tool path worked out, so that it can be reused without having to do it all again, for future similar genbank datasets. You may even want to publish the workflow for others to use, as it is very popular request, maybe add published page to explain how to use/prep data for input. Apologies for the current inconvenience, but hopefully this can get you going until a more direct method is implemented directly in Galaxy main. Great idea that many other users are also very interested in. Any contributions (page, workflow) would be most welcomed. A tool that does the extraction directly from Genbank would also be welcomed in the Tool Shed, if you want to contribute. http://community.g2.bx.psu.edu/ Best, Jen Galaxy team On 3/14/11 1:15 PM, David Matthews wrote: Hi again, Does anyone know of a genbank to gtf converter? I have heard such things exist but never found one... Cheers David ___ 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 ___ 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/
[galaxy-user] Tophat version
Hi, Just wondering when the tophat portion of Galaxy will be updated? Its currently version 1.1.1 and there is now a version 1.2.0 (in fact I think there have been 4 updates). Cheers David ___ 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/
Re: [galaxy-user] downstream analysis of cuffdiff out put
Hi All, I agree with this problem and solution. I have a lot of cufflinks, cuffcompare and cuffdiff output but I am struggling to relate what this means in terms of the real world! I have seen partek software attempt to visualise some of the data it generates which appears to be using the FMI data in the cufflinks suite but beyond that I struggle. I did have an email conversation with Cole Trapnell which eventually centred on the idea that you just have to trust the analysis and then go away and do the RT-PCR to check it all out! So for tools I think: 1. A tool that shows you the layout of known isoforms for a gene and the FMI data for each isoform. er. thats it for now from me! But I also struggle to understand what all the other outputs really mean! What does the CDS.diff output tell us? What dies the promoters.diff output tell us? I know what the cufflinks manual says but I struggle to convert this in my head to what is happening to an actual gene so if anyone has a power point example on a specific gene of what the data is saying in terms of how this relates to changes in protein production - that would be great! I'm hoping someone out there has had to lecture on this to students and they have done a powerpoint presentation and are willing to show it to the galaxy community. Another point about the analysis of cufflinks data is the subject of the Pseudo Autosomal Regions in X and Y - this will make a mess of gene expression analysis in some cases especially because tophat will assign a read to both sites and make it a multihit read (which you might then filter out) or it may double the true levels of reported expression.. Anyone had thoughts on this? 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.matth...@bristol.ac.uk On 10 Mar 2011, at 15:55, Jeremy Goecks wrote: Jagat, Please send queries such as these to the galaxy-user mailing list (cc'd); there are many users on the list who can contribute to this discussion, and there are many additional users that will benefit from this discussion. I was wondering if you can point me to a documentation or URL to guide how to perform the downstream analysis once we have cuffdiff out put. In general, I agree that tools are needed to further process cufflinks/compare/diff outputs, but I'm not aware of any that are publicly available. Let's open this issue up for discussion and see if we can reach a consensus about tools might be useful. Everyone, please feel free to contribute ideas/tools; note that the Galaxy Tool Shed is a nice place for sharing tools you've built for Galaxy: http://community.g2.bx.psu.edu/ 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. Best, J. ___ 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/ ___ 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/
[galaxy-user] Pseudo Autosomal regions in Chrs X and Y
Hi All again, A separate point about the analysis of cufflinks data is the subject of the Pseudo Autosomal Regions in X and Y - this will make a mess of gene expression analysis in some cases especially because tophat will assign a read to both places which therefore makes it a multihit read (which you might then filter out) or it may double the true levels of reported expression. Anyone had experience/thoughts on this? 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.matth...@bristol.ac.uk ___ 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/
Re: [galaxy-user] how to find out the gene_ID correspond to CUFF ID
Hi, Yes, column 1 refers to the chromosome name and it must be the same throughout (i.e. your hg19 reference file must call the chromosomes 1,2, 3 etc). A simpler solution is to use a copy of hg19 that lists the chromosomes as 1, 2, 3 etc instead of Chr1, Chr2 etc. Unfortunately I'm only in intermittent contact with the web - I might be able to help you properly next week when I am back at work. However, I've just publicly shared a history containing a hg19 file, a female hg19 (missing chromosome Y) and an ensembl gtf file that all work together (i.e. all use the same names for the chromosomes!) called Bristol hg19... just look under shared data. However, you will probably need to repeat your tophat alignments using your reads and these files together. Good luck! David On 1 Mar 2011, at 20:06, Ying Zhang wrote: Dear Vasu: thank you for your information! I have checked the reference and do not find a specific column that include chromosome information, do you mean the first column(seqname)? Do you happen to have one with correct format and I can used for reference annotation? Thanks a lot! I onlg have limited experience in computing so I do not know how to format this file. Best Ying Quoting vasu punj pu...@yahoo.com: I believe you need to format the Ensemble file Chromosome columns is not correct. Vasu --- On Tue, 3/1/11, Ying Zhang ying.zhang.yz...@yale.edu wrote: From: Ying Zhang ying.zhang.yz...@yale.edu Subject: Re: [galaxy-user] how to find out the gene_ID correspond to CUFF ID To: David Matthews d.a.matth...@bristol.ac.uk Cc: galaxy-u...@bx.psu.edu Date: Tuesday, March 1, 2011, 10:59 AM Dear David: I followed your advices and downloaded reference sequence from Emsemble, then I uploaded this file into galaxy, and then I run the cufflinks using the file as a reference annotation, however I got error when I am running, the following the error message gave to me: An error occurred running this job: cufflinks v0.9.3 cufflinks -I 30 -F 0.05 -j 0.05 -p 8 -Q 0 -G /galaxy/main_database/files/002/122/dataset_2122219.dat -r /galaxy/data/hg19/sam_index/hg19.fa Error running cufflinks. [11:47:14] Loading reference and sequence. GFF warning: mergi Do you have any idea of what is going wrong here? Best Ying Quoting David Matthews d.a.matth...@bristol.ac.uk: Hi, Yeah, thats a good idea too!! I did not know about that tool, shows what I know (!) - thanks for the info! Cheers David On 1 Mar 2011, at 04:51, Jeremy Goecks wrote: Ying, you could also try using the tools 'Fetch closest non-overlapping feature' and 'Intersect' to find genes nearby transcripts/genes/TSSes of interest; for both tools, you'll want a reference annotation, either from UCSC or Ensembl. Best, J. On Feb 28, 2011, at 6:10 PM, David Matthews wrote: Hi, You need to supply a gene annotation file with cufflink to easily get the gene-id information. Without it, cufflinks simply tries its best to figure out what genes are present. The ensemble gtf file is quite a comprehensive one - there is a link to it on the cufflinks manual page. Good luck! David On 28 Feb 2011, at 21:33, Ying Zhang wrote: Dear Everyone: I have got one output file after I run Cufflink which contain gene expression information. However, I found out for each gene_ID, it has the format like, CUFF.1151175, do you have idea of how to find out the offical gene ID correspond to this CUFF ID? Thank you very much! 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/ ___ 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 ___ The Galaxy User list should be used
Re: [galaxy-user] how to find out the gene_ID correspond to CUFF ID
Hi, You need to supply a gene annotation file with cufflink to easily get the gene-id information. Without it, cufflinks simply tries its best to figure out what genes are present. The ensemble gtf file is quite a comprehensive one - there is a link to it on the cufflinks manual page. Good luck! David On 28 Feb 2011, at 21:33, Ying Zhang wrote: Dear Everyone: I have got one output file after I run Cufflink which contain gene expression information. However, I found out for each gene_ID, it has the format like, CUFF.1151175, do you have idea of how to find out the offical gene ID correspond to this CUFF ID? Thank you very much! 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/ ___ 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/
[galaxy-user] RNA seq analysis
Hi Jeremy, I thought I'd write to get a discussion of a workflow for people doing RNA seq that I have found very useful and addresses some issues in mapping mRNA derived RNA-seq paired end data to the genome using tophat. Here is the approach I use (I have a human mRNA sample deep sequenced with a 56bp paired end read on an illumina generating 29 million reads): 1. Align to hg19 (in my case) using tophat and allowing up to 40 hits for each sequence read 2. In samtools filter for read is unmapped, mate is mapped and mate is mapped in a proper pair 3. Use group to group the filtered sam file on c1 (which is the bio-sequencer read number) and set an operation to count on c1 as well. This provides a list of the reads and how many times they map to the human genome, because you have filtered the set for reads that have a mate pair there will be an even number for each read. For most of the reads the number will be 2 (indicating the forward read maps once and the reverse read maps once and in a proper pair) but for reads that map ambiguously the number will be multiples of 2. If you count these up I find that 18 million reads map once, 1.3 million map twice, 400,000 reads map 3 times and so on until you get down to 1 read mapping 30 times, 1 read mapping 31 times and so on... 4. Filter the reads to remove any reads that map more than 2 times. 5. Use compare two datasets to compare your new list of reads that map only twice to pull out all the reads in your sam file that only map twice (i.e. the mate pairs). 6. You'll need to sort the sam file before you can use it with other applications like IGV. What you end up with is a sam file where all the reads map to one site only and all the reads map as a proper pair. This may seem similar to setting tophat to ignore non-unique reads. However, it is not. This approach gives you 10-15% more reads. I think it is because if tophat finds (for example) that the forward read maps to one site but the reverse read maps to two sites it throws away the whole read. By filtering the sam file to restrict it to only those mappings that make sense you increase the number of unique reads by getting rid of irrational mappings. Has anyone else found this? Does this make sense to anyone else? Am I making a huge mistake somewhere? A nice aspect of this (or at least I think so!) is that by filtering in this manner you can also create a sam file of non-unique mappings which you can monitor. This can be useful if one or more genes has a problem of generating a lot of non-unique maps which may give problems accurately estimating its expression. Also, you also get a list of how many multi hits you have in your data so you know the scale of the problem. 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.matth...@bristol.ac.uk ___ 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/
Re: [galaxy-user] get wig file after tophat
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.matth...@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.matth...@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.yz...@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
Re: [galaxy-user] get wig file after tophat
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.yz...@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/
[galaxy-user] Stalled cuffdiff run
Hi Jeremy, I have a stalled cufflinks run - its been queued all day - any idea why its stalled? Cheers 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 d.a.matth...@bristol.ac.uk ___ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
