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Pre_filtering of 10X RNAseq loom data from velocyto.py

Open SiyiWanggou opened this issue 4 years ago • 1 comments

Hi velocyto-team, Velocyto.py is a powerful pipline for single cell RNAseq analysis, thanks a lot to your excellent job. I'm fresh in RNA velocity ananlysis and recently I met some issue about my dataset. I used seurat_wrappers to load the loom file and did a Knee_plot of spliced and unspliced matrices. I found that for spliced matrix, the minium total UMIs is 100. My question is, for 10x RNAseq data generated from cellranger, is the empty droplets have already be filtered in final loom file?

Thanks,

SiyiWanggou avatar Mar 10 '20 19:03 SiyiWanggou