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Old 06-22-2011, 09:04 AM   #5
Peter (Biopython etc)
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,542

Tophat may not look at the qualities, but it does write them out in the SAM/BAM file. This is important because if Tophat misunderstood the input FASTQ encoding, they will be wrong in the SAM/BAM.

It would be worth double checking a couple of reads - compare the input quality (which you say used the Solexa/Illumina 1.3 style, meaning PHRED with offset 64) and the SAM/BAM quality (which should be Sanger style, meaning PHRED with offset 33).

[Given Tophat doesn't look at the read qualities, this is a separate issue to your original query about the mapping qualities]
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