search

cortes-ciriano-lab / SComatic

A tool for detecting somatic variants in single cell data
Other
145 stars 20 forks source link

Why is the default value of the parameter "min_mq" 255 #39

Closed Topigs closed 6 months ago

Topigs commented 8 months ago

Thanks so much for such a wonderful tool！ In view the script "scripts/BaseCellCounter/BaseCellCounter py", I am very confused with the default value of the command line option "-- min_mq". Why set it to 255 instead of something more reasonable, I mean like 30.

Francesc-Muyas commented 6 months ago

Dear user, Thanks for using SComatic. This default mapping quality is ideal for detecting uniquely mapping reads in scRNA-seq data (usually aligned with STAR).

-- min_mq 30 would be a better parameter for DNA-based approaches like scATAC-seq.

Thanks, Fran