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babakshaban

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babakshaban
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  • Hi, shlee. I tried the commands in that post and I still received an error. I performed a QualityDistribution with picard and I attached the pdf below. Does the Quality score distribution chart account for scores above 40? I used both the -fixMise…
  • Hi Sheila, It's not an issue with low quality scores, it's an issue with the quality scores. The fastqc revealed a graph with no quality score under Q30. I tried looking for any documentation that mentions issues with different types of encoding a…
  • Hi, OK. So I was able to get it "working" but I still don't really understand why. I checked, double, triple checked the encoding. I was told they were solexa1.3 encoding but every check was coming up as illumina 1.9. I then converted th…
  • Hi, I should add that the samples I used were from here: https://www.ncbi.nlm.nih.gov/sra/SRX690960[accn] and https://www.ncbi.nlm.nih.gov/sra/SRX690946[accn] and the reference from the link below. http://hgdownload.soe.ucsc.edu/goldenPath/panTr…
  • That would be great, Thanks! Bobbie
  • Hi Sheila, I changed the -mmq to 0 and it's still the same. I know the quality of the files are very good as I have checked them in fastqc. I run the same pipeline with "poorer" quality reads and they work fine. They are 75 and 125 bp len…