Generating Pileup For Snp Analysis

Question: Generating Pileup For Snp Analysis

7.8 years ago by

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

galaxy • 1.0k views

ADD COMMENT • link •

modified 7.8 years ago by Jennifer Hillman Jackson ♦ 25k • written 7.8 years ago by Christine Picard • 10

7.8 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k 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 -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org

ADD COMMENT • link written 7.8 years ago by Jennifer Hillman Jackson ♦ 25k

7.8 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

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 -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org

ADD COMMENT • link written 7.8 years ago by Jennifer Hillman Jackson ♦ 25k

7.8 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

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 -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org

ADD COMMENT • link written 7.8 years ago by Jennifer Hillman Jackson ♦ 25k

Please log in to add an answer.

Similar posts • Search »