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Old 07-11-2014, 03:26 AM   #2
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Location: Montreal

Join Date: May 2013
Posts: 367

Your argument that TopHat has changed the quality scores would be more convincing if you posted the same sequence before and after alignment with TopHat.
You've posted two different sequences, with obviously different quality scores.
Can you post the same sequence, before and after alignment with TopHat?

TopHat2 does have optional arguments to handle quality scores in the Solexa scale, incidentally.

--solexa-quals Use the Solexa scale for quality values in FASTQ files.
--solexa1.3-quals As of the Illumina GA pipeline version 1.3, quality scores are encoded in Phred-scaled base-64. Use this option for FASTQ files from pipeline 1.3 or later.
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