Tophat Quality Scale

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

tophat

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updated 14.0 years ago by JC

• written 14.0 years ago by narges •

1 answer

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.

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written 14.0 years ago by JC

Thank you so much

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written 14.0 years ago by narges •

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