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MikeAxtell / ShortStack

ShortStack: Comprehensive annotation and quantification of small RNA genes
MIT License
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Corrected bowtie options #73

Closed zajakin closed 1 year ago

zajakin commented 6 years ago

Corrected bowtie options

MikeAxtell commented 6 years ago

Hi Pawel, thanks for the pull request. I see you want to allow alignments with up to 3 mismatches. I'm not so sure about that. A while back I recall doing some testing that seemed to suggest that 3 or more mismatches was giving quite rates of false alignments. For a 21 mer, that means just 18 out of 21 nts matching. Have you done any testing that tries to quantify false positive rates when 3 mismatches are allowed?

Best and thanks for your contribution!