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Published 20 hours ago • verified publisher icon t-neumann

Question about "-e" parameter

Open bocheng97 opened this issue 3 years ago • 1 comments

Hi,

I am dealing with quant-seq data, and I was wondering if I should use "-e" or not, also can you explain the description of "-e" in the DOCS, "Deactivates NextGenMap’s SLAMSeq alignment settings. Can be used to align plain QuantSeq data instead of SLAMSeq data."? THank you

bocheng97 avatar Jul 28 '22 20:07 bocheng97

Hi,

if you have plain unlabelled QuantSeq data (no T>C conversions), then you should use -e to disable the alternative base scoring scheme we established for SLAM-seq data.

t-neumann avatar Jul 29 '22 09:07 t-neumann