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nf-core / crisprseq

A pipeline for the analysis of CRISPR edited data. It allows the evaluation of the quality of gene editing experiments using targeted next generation sequencing (NGS) data (`targeted`) as well as the discovery of important genes from knock-out or activation CRISPR-Cas9 screens using CRISPR pooled DNA (`screening`).
https://nf-co.re/crisprseq
MIT License
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Sample not being detected as edited despite evidence of editing in the bam file #188

Open alan-tracey opened 4 months ago

alan-tracey commented 4 months ago

Description of the bug

I’ve run this pipeline now with a few hundred samples - generally it seems to be working very well. However, I notice that one sample which clearly shows editing in the bam file, is not being detected as edited. Looking at the indels QC file, almost all the reads are not passing filter. However, I can’t see from the bam file why it shouldn’t be passing filter.

Screenshot 2024-07-09 at 13 25 58

Command used and terminal output

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Relevant files

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System information

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alan-tracey commented 4 months ago

In case it helps to see this zoomed in further

Screenshot 2024-07-25 at 16 02 44