Giters

r3fang / SnapATAC

Analysis Pipeline for Single Cell ATAC-seq

Geek Repo:Geek Repo

Github PK Tool:Github PK Tool

Weird promoter ratio versus log10(UMI) curve

strawberry789 opened this issue · comments

commented

This is what my promoter ratio versus log10(UMI) curve looks like:

image

What's wrong with this? And how should I select the quality barcodes based on this graph? I tried to set low quality criteria, but result in zero cell barcodes after filtering.

Thank you.

commented

图片
For custom references or references missing the promoter.bed file, the count of promoter_region_fragments is 0. I use TSS_fragments to filter cell barcodes instead.

commented

My promoter ratio plots were exactly the same as yours 🌚, although my reference genome version is hg38, of which the bed file should not be missing, this is weird. I instead use the peak ratio combined with logUMI as QC metrics.