- galaxy-user - lists.galaxyproject.org

extract alignment for a set of genes
by Vincent Joseph Lynch 10 Jun '11

10 Jun '11

To Whom It May Concern, Sorry to bother you with what is likely a fairly simple problem, but I have trying to figure this out myself for several days and just can't figure out how to do it. I have a set of 8766 genes that I would like to test for positive selection in using various other programs (HyPhy for example). To do this I obviously need an alignment of these genes across various species, but I just can't figure out how to get the alignment in a fasta format. For example, I have a BED12 file from UCSC with the data for the 8766 genes, I thought the easiest way was to use the "Stitch Gene blocks" option and then select locally cached alignments as the MAF source for the species I care about. However, because these 8766 genes have multiple transcripts I end up with 23,581 regions. Is there a way to merge the multiple regions for each gene into a single region for the longest transcript? Then I should have 8766 regions and can use Stitch Gene blocks". (Unless there is a more economical way to do this.)\ Thanks Vinny Vincent J. Lynch, Associate Research Scientist Department of Ecology and Evolutionary Biology & Yale Systems Biology Institute Yale University http://pantheon.yale.edu/~vjl4/profpage/ "There is a grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that whilst this planet has gone on cycling according to the fixed laws of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved." -C. Darwin, 1859 (Walker, Wisconsin, Madison, Maddow, Tea Party, Obama, global warming)

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program for filtering and trimming data
by Joanne Rampersad 10 Jun '11

10 Jun '11

Hi Is there an stand alone ( ie not a component of Bowtie etc ) program in galaxy that can filter or trim fastq data? thanks

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substring sequence on coordinate in columns
by Michal Stuglik 10 Jun '11

10 Jun '11

Hi all, I am wondering if galaxy has tool to substring/extract sequence/text from another sequence/text based on coordinates in columns (start, end column) or how to do it in Text Manipulation/Compute? all the best, michal

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Converting transcriptomes to proteomes
by David Matthews 10 Jun '11

10 Jun '11

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.Matthews(a)bristol.ac.uk

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Galaxy tool error report from johnwu@ibms.sinica.edu.tw
by galaxy-user＠lists.bx.psu.edu 09 Jun '11

09 Jun '11

GALAXY TOOL ERROR REPORT ------------------------ This error report was sent from the Galaxy instance hosted on the server "192.168.0.36:8080" ----------------------------------------------------------------------------- This is in reference to dataset id 377 from history id 2 ----------------------------------------------------------------------------- You should be able to view the history containing the related history item 176: Cuffcompare on data 175: transcript accuracy by logging in as a Galaxy admin user to the Galaxy instance referenced above and pointing your browser to the following link. 192.168.0.36:8080/history/view?id=f597429621d6eb2b ----------------------------------------------------------------------------- The user 'johnwu(a)ibms.sinica.edu.tw' provided the following information: While executing cuffcompare, I encountered this error message: Error running cuffcompare. [Errno 2] No such file or directory: 'cc_output' I was practicing RNA-seq analysis steps on newly installed galaxy to test if i could easily analyze my data. I could run cufflinks and cuffdiff through galaxy, but i'm unable to run cuffcompare. how should i solve this problem? thanks a lot! ----------------------------------------------------------------------------- job id: 126 tool id: cuffcompare ----------------------------------------------------------------------------- job command line: python /home/galaxy/software/galaxy_dist/tools/ngs_rna/cuffcompare_wrapper.py -s --ref_file="None" --dbkey=hg19 --index_dir=/home/galaxy/software/galaxy_dist/tool-data /home/galaxy/software/galaxy_dist/database/files/000/dataset_376.dat ----------------------------------------------------------------------------- job stderr: Error running cuffcompare. [Errno 2] No such file or directory: 'cc_output' ----------------------------------------------------------------------------- job stdout: cuffcompare v1.0.3 (2403) cuffcompare -o cc_output -s /home/galaxy/data/galaxy_data/sam_index/hg19.fa ./input1 ----------------------------------------------------------------------------- job info: None ----------------------------------------------------------------------------- job traceback: None ----------------------------------------------------------------------------- (This is an automated message).

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Aligning against Multiple Reference Sequences
by John David Osborne 09 Jun '11

09 Jun '11

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

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Cufflinks error in galaxy
by 吳正華 09 Jun '11

09 Jun '11

Hi galaxy dev team: I just installed galaxy on my ubuntu box and tried to do RNA-seq analysis according to Jeremy's excellent tutorial http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise however, I encountered following error messages when I was trying to execute Cufflinks in galaxy.. Dataset generation errors Dataset 121: Cufflinks on data 92: gene expression Tool execution generated the following error message: Error running cufflinks. [Errno 2] No such file or directory: 'transcripts.gtf' The tool produced the following additional output: cufflinks v1.0.3 cufflinks -q --no-update-check -I 300000 -F 0.050000 -j 0.050000 -p 4 -b how should I solve this problem? Thanks in advance. Best Regards, John Wu

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FastQ Groomer and Compute Quality Statistics
by John David Osborne 09 Jun '11

09 Jun '11

I noticed that for our new Ilumina data (which generate Sanger format) the FastQ groomer output is identical to the Ilumina FastQ input file. I was hoping to go ahead and just use the raw FastQ files as input (saving disk space) for computing quality statistics to look at box plots, but it appears that the tool "Compute Quality Statistics" appears to require that the data have been run through FastQ Groomer first. Is there a way to get around this and is this a bug? I assuming this is some sort of safety measure built into this tool? -John

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LASTZ arguments in "Full parameter list"-mode
by Appelt, Uwe 09 Jun '11

09 Jun '11

Hi @All, short version: Is it possible to specify more arguments in "Full parameter list"-mode, particularly those that're implicitely described in YASRA-mode (match/mismatch rewards and step-size (Z/step))? long version: I'm dealing with 454 reads and it's crucial to the scenario to have the 5' ends aligned properly (in terms of sensitivity), so all the YASRA-templates comprising heavy gap penalties perform fairly poor as soon as there's a gap nearby the 5' end. However, heading to "Full parameter list"-mode leads to excessive CPU-use, because (presumably) the step-size (default=1?) is left unset. Also, it'd be great to be able to alter not only gap penalties, but match/mismatch rewards as well. (Obviously a mismatch would cause the same problem). Examples: AAAAAAAAAA (target) AAAAATAAAA (query) => I need the alignment boundary to be found at position 1, rather than behind the mismatched T and this cleary doesn't work as long as the mismatch penalty is too large (same applies for gap-open/extend penalties). Thanks in advance and Cheers, Uwe

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Galaxy tool error report from johnwu@ibms.sinica.edu.tw
by "mailto:galaxy-user"＠lists.bx.psu.edu 09 Jun '11

09 Jun '11

GALAXY TOOL ERROR REPORT ------------------------ This error report was sent from the Galaxy instance hosted on the server "192.168.0.36:8080" ----------------------------------------------------------------------------- This is in reference to dataset id 316 from history id 2 ----------------------------------------------------------------------------- You should be able to view the history containing the related history item 121: Cufflinks on data 92: gene expression by logging in as a Galaxy admin user to the Galaxy instance referenced above and pointing your browser to the following link. 192.168.0.36:8080/history/view?id=f597429621d6eb2b ----------------------------------------------------------------------------- The user 'johnwu(a)ibms.sinica.edu.tw' provided the following information: Hi galaxy dev team: I just installed galaxy on my ubuntu box and tried to do RNA-seq analysis according to Jeremy's excellent tutorial http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise however, I encountered following error messages when I was trying to execute Cufflinks in galaxy.. ----------------------------------------------------------------------------- job id: 106 tool id: cufflinks ----------------------------------------------------------------------------- job command line: python /home/galaxy/software/galaxy_dist/tools/ngs_rna/cufflinks_wrapper.py --input=/home/galaxy/software/galaxy_dist/database/files/000/dataset_287.dat --assembled-isoforms-output=/home/galaxy/software/galaxy_dist/database/files/000/dataset_318.dat --num-threads="4" -I 300000 -F 0.05 -j 0.05 -b --ref_file="None" --dbkey=hg19 --index_dir=/home/galaxy/software/galaxy_dist/tool-data ----------------------------------------------------------------------------- job stderr: Error running cufflinks. [Errno 2] No such file or directory: 'transcripts.gtf' ----------------------------------------------------------------------------- job stdout: cufflinks v1.0.3 cufflinks -q --no-update-check -I 300000 -F 0.050000 -j 0.050000 -p 4 -b ----------------------------------------------------------------------------- job info: None ----------------------------------------------------------------------------- job traceback: None ----------------------------------------------------------------------------- (This is an automated message).

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