what strategy is applied to select CB

Hoohm / dropSeqPipe

A SingleCell RNASeq pre-processing snakemake workflow

Creative Commons Attribution Share Alike 4.0 International

147 stars 47 forks source link

what strategy is applied to select CB #107

Open YOU-k opened 4 years ago

YOU-k commented 4 years ago

Hi, I both ran dropseqpipe and Cellranger with emptydrops, but i just find that the cells selected quite differ. I would like to know what exactly you applied to select true cells from ambient RNA. Thanks!

Hoohm commented 4 years ago

Hey @YOU-k Our filters are based on either a provided whitelist or on the number of cells provided in the sample.csv file.

We don't perform any selection based on expression values for example. We prefer letting the user decide so that we don't skew the data as consensus on filtering is not totally stable yet.