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Finding off target regions
Nima Mousavi edited this page May 28, 2019
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This page describes the usage of a script to find the off-target regions associated with a motif. The script and helpers are available in GangSTR/scripts/extract_offtarget. The extracted off-target regions will be printed in stdout.
cd GangSTR/scripts/extract_offtarget
python run.py <motif> <ref_genome.fa> <temp_dir/> <num_reads>
This script uses bwa-mem and wgsim
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motif: The TR repeating element, (i.e.,CAG) -
ref_genome.fa: Path to reference genome fasta -
temp_dir/: Path to a directory to store temporary files -
num_reads: Number of simulated reads