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r3fang / SnapATAC

Analysis Pipeline for Single Cell ATAC-seq
GNU General Public License v3.0
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Weird promoter ratio versus log10(UMI) curve #222

Open strawberry789 opened 3 years ago

strawberry789 commented 3 years ago

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.

ChenManqi2 commented 2 years ago

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.

murphchuyi commented 2 years ago

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.