Generating pileup for SNP analysis
I am a new user to Galaxy, and I was hoping someone might be able to help with this small problem. I am using Drosophila resequencing data downloaded from the SRA and trying to look for SNPs that differentiate the two strains. I've gotten as far as generating the pileup for each strain, but my column which has the consensus base is always an N. Can anyone help me out? thanks, Christine -- Christine J. Picard, Ph.D. Postdoctoral Research Associate Department of Entomology Texas A&M University TAMU 2475 College Station, TX 77843-2475 christine.picard@gmail.com
Hi Christine, Would you like to share a link to your history? Use Options -> Share or Publish and we can take a look at the input data (likely the source of problem). Best, Jen Galaxy team On 2/11/11 7:20 AM, Christine Picard wrote:
I am a new user to Galaxy, and I was hoping someone might be able to help with this small problem. I am using Drosophila resequencing data downloaded from the SRA and trying to look for SNPs that differentiate the two strains. I've gotten as far as generating the pileup for each strain, but my column which has the consensus base is always an N. Can anyone help me out?
thanks, Christine
-- Christine J. Picard, Ph.D. Postdoctoral Research Associate Department of Entomology Texas A&M University TAMU 2475 College Station, TX 77843-2475 christine.picard@gmail.com <mailto:christine.picard@gmail.com>
_______________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
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-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org
Hello Christine, We have confirmed that the reads have Sanger qual format, not Illumina (as were originally run in your history) or Solexa (as some are at NCBI, from other SRA projects, but not this one). Please re-run the Fastq groomer with Sanger as the input type and all should run correctly. Thank you again for working with us to resolve the issue and for using Galaxy! Please let us know if we can help more or if the results after the re-run are not what you expect. Best, Jen Galaxy team On 2/11/11 7:20 AM, Christine Picard wrote:
I am a new user to Galaxy, and I was hoping someone might be able to help with this small problem. I am using Drosophila resequencing data downloaded from the SRA and trying to look for SNPs that differentiate the two strains. I've gotten as far as generating the pileup for each strain, but my column which has the consensus base is always an N. Can anyone help me out?
thanks, Christine
-- Christine J. Picard, Ph.D. Postdoctoral Research Associate Department of Entomology Texas A&M University TAMU 2475 College Station, TX 77843-2475 christine.picard@gmail.com <mailto:christine.picard@gmail.com>
_______________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. 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:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org
participants (2)
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Christine Picard -
Jennifer Jackson