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Old 06-22-2011, 08:57 AM   #2
Peter (Biopython etc)
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,542

Originally Posted by jjpurwar View Post
I have been trying to work with the sam output file that I received from tophat. My input file was an RNA-sequencing single end 36 bp run using Illumina GA2 with C. elegans data.
Whenever the is something funny going on with quality scores, the first thing I try to check is what kind of FASTQ encoding did you start with (Sanger, old Solexa, or Illumina). And did you tell tophat this, or just trust the default was appropriate?
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