Closed IgorUlitsky closed 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.
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 :)