Re: [galaxy-user] Generating pileup for SNP analysis

22 Feb 2011

      Hello Christine,

The data issue goes back to the initial grooming step. When using "Fastq 
Groomer", choose "Solexa" instead of "Illumina 1.3+" as the Input FASTQ 
quality score type. This preserves the correct quality score 
translation, which was the root of the problem in the derivative steps.

Hopefully this helps when you do the re-run of the analysis, but please 
let us know if we can help more. I'll send you a link off-line to a 
history with some more specific information to your project,

Thanks,

Jen
Galaxy team
...
On Wed, Feb 16, 2011 at 9:10 AM, Jennifer Jackson <jen@bx.psu.edu
<mailto:jen@bx.psu.edu>> wrote:
Hi Christine,
Would you like to share a link to your history? Use Options -> Share
    or Publish and we can take a look at the input data (likely the
    source of problem).
Best,
Jen
    Galaxy team
On 2/11/11 7:20 AM, Christine Picard wrote:
I am a new user to Galaxy, and I was hoping someone might be able to
        help with this small problem.  I am using Drosophila
        resequencing data
        downloaded from the SRA and trying to look for SNPs that
        differentiate
        the two strains.  I've gotten as far as generating the pileup
        for each
        strain, but my column which has the consensus base is always an
        N.  Can
        anyone help me out?
thanks, Christine
--
        Christine J. Picard, Ph.D.
        Postdoctoral Research Associate
        Department of Entomology
        Texas A&M University
        TAMU 2475
        College Station, TX
        77843-2475
        christine.picard@gmail.com <mailto:christine.picard@gmail.com>
        <mailto:christine.picard@gmail.com
        <mailto:christine.picard@gmail.com>>
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--
    Jennifer Jackson
    http://usegalaxy.org
    http://galaxyproject.org
--
Christine J. Picard, Ph.D.
Postdoctoral Research Associate
Department of Entomology
Texas A&M University
TAMU 2475
College Station, TX
77843-2475
christine.picard@gmail.com <mailto:christine.picard@gmail.com>
-- 
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org