Tophat Quality Scale

Question

[narges]

hello, I wanted to know your idea that in an rna seq analysis, when running tophat over an illumina datset, should I rely on the quality scale the tophat obtain automatically or I should obtain it before the analysis and if I should any suggestion about how to get it? many thanks

Answer 1

[JC]

You should not modify the read quality score per base, Tophat/Bowtie can be run with specific parameters for different quality score scales. If you mean mapping quality score, then you should not modify it unless you really understand what are you doing.

[narges]

Thank you so much