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Weird promoter ratio versus log10(UMI) curve

Open strawberry789 opened this issue 4 years ago • 2 comments

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.

strawberry789 avatar Mar 03 '21 07:03 strawberry789

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.

ChenManqi2 avatar Nov 19 '21 13:11 ChenManqi2

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.

murphchuyi avatar Mar 16 '22 08:03 murphchuyi