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t-neumann / slamdunk

Streamlining SLAM-seq analysis with ultra-high sensitivity
GNU Affero General Public License v3.0
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Question about "-e" parameter #115

Closed bocheng97 closed 4 months ago

bocheng97 commented 2 years ago

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

t-neumann commented 2 years ago

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.