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lehner-lab / DiMSum

An error model and pipeline for analyzing deep mutational scanning (DMS) data and diagnosing common experimental pathologies
MIT License
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Clarify --maxSubstitutions argument #13

Closed ijhoskins closed 1 year ago

ijhoskins commented 1 year ago

Hello @andrefaure

Docs say "--maxSubstitutions Maximum number of nucleotide or amino acid substitutions for coding or non-coding sequences respectively (default:2)"

I was slightly confused with the word 'respectively' and its relation to the first phase. Could you confirm this means that (by default), in noncoding mode, sequences with more than 2 nt mismatches are discarded; and for coding mode, sequences with more than 2 amino acid changes are discarded?

andrefaure commented 1 year ago

Hi @ijhoskins yes that's correct.