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



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