Hi! I want to analyse data from a CRISPR/Cas9 screen (control vs. treatment) and I'm using Mageck (https://sourceforge.net/projects/mageck/). The sequencing was performed using Illumina (paired-end).
The problem is that I've noticed that in R1 fastq files the half of the reads containing the sgRNA are R2 (in R2 files there are R1 reads as well). Should I consider these reads in the sgRNA count?.