## CRISPRanto

A (Snakemake) pipeline for CRISPR offtarget detection

Used in Raitskin et al. (2018?)

Requirements

• Python3.5+ with latest Snakemake
• ktio (pip install ktio)
• jellyfish 2 (e.g. jellyfish-2.2.6)
• bbmap >= 38.06
• bedtools >= 2.26.0
• if on Mac: GNU versions of sed, awk, join

Data for Raitskin et al.

• TAIR10 gene annotation https://www.arabidopsis.org/download_files/Genes/TAIR10_genome_release/TAIR10_gff3/TAIR10_GFF3_genes.gff
• TAIR10 chromosomes https://www.arabidopsis.org/download_files/Sequences/TAIR10_blastsets/TAIR10_seq_20101214_updated
• Use these data to extract all sequences of CDS (i.e. coding part of exon) features
• Functional annotation E.g. from https://www.arabidopsis.org/download_files/Genes/TAIR10_genome_release/TAIR10_functional_descriptions
• Need 2-column tab-separated file: AGI,Function(with space replaced by "_")