search

pinellolab / CRISPResso2

Analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments
Other
274 stars 95 forks source link

CRISPRessoWGS unable to map reads #145

Closed IgorUlitsky closed 3 years ago

IgorUlitsky commented 3 years ago

I'm trying to run CRISPRessoWGS with some data obtained by Nextera of specific amplicons. Tried both the amplicon mode and the WGS mode, and the WGS mode aligning to the genome or to the amplicons, but in all cases, getting "has too few reads mapped to it (0)! Not running CRISPResso! " for all the segments, even though there are reads aligned to them. I've placed all the input files here: ftp://ftp-igor.weizmann.ac.il/pub/crispresso/

This is the command I'm running: CRISPRessoWGS -b IIC_locLib_S2.hg19.sorted.bam -f regions.bed -r /home/labs/ulitsky/shared/data/human/sequence/hg19.fa --name IIC_locLib

Please advise :)

kclem commented 3 years ago

I quickly checked your input, the problem is that the regions specified in the bed files are too large.

CRISPRessoWGS can process only reads that fully cover the region defined in the bed file, please try to use smaller regions e.g. 40-50bp around the expected cleavage sites, this should fix the problem. If you have longer read length in your WGS data (e.g. 150bp) you may increase this, however the number of reads aligned may drop.