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 <j...@bx.psu.edu
<mailto:j...@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.pic...@gmail.com <mailto:christine.pic...@gmail.com>
        <mailto:christine.pic...@gmail.com
        <mailto:christine.pic...@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
        <http://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/


    --
    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.pic...@gmail.com <mailto:christine.pic...@gmail.com>


--
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. 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/

Reply via email to