CRISPR Library Sequencing Analysis

The analysis for this paper was performed on 81 M raw reads from Illumina deep sequencing collected following the addition of the small molecule dTAG-47 at four time points to a CRISPR library consisting of 48 well-characterized guide sequences. Sequencing reads were filtered to remove low-quality (Illumina average quality <28) or unmapped reads and were genotyped. For each sequencing read representing a CRISPR-Cas9 cutting event, the cutting genotype was identified and categorized as an insertion or deletion event, and overall fractions of insertions and deletions of all lengths were computed for two replicates at each different time point. The analysis protocol was described previously.^{38 (link)}