Run emptyDrops for each sample instead of all combined - Githubissues

LieberInstitute / DLPFC_snRNAseq

snRNA_seq portion of the spatialDLPFC project

http://research.libd.org/spatialDLPFC/

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Run emptyDrops for each sample instead of all combined #3

Closed lcolladotor closed 2 years ago

lcolladotor commented 2 years ago

@mattntran @lahuuki @abspangler13 and I checked some of the plots like at:

Screen Shot 2021-12-10 at 1 22 01 PM

[ ] lapply() over emptyDrops() similar to https://github.com/LieberInstitute/10xPilot_snRNAseq-human/blob/master/10x_all-FACS-n10_2021rev_step01_processing-QC_MNT.R#L99 instead of https://github.com/LieberInstitute/DLPFC_snRNAseq/blob/main/code/03_build_sce/droplets.R#L18-L25
[ ] still save a single sce like at https://github.com/LieberInstitute/DLPFC_snRNAseq/blob/main/code/03_build_sce/droplets.R