CRISPR off-target sequencing analysis

Published: 19-09-2017| Version 2 | DOI: 10.17632/6r7spc5x6f.2
Contributors:
Zuzana Tothova,
John Krill-Burger,
Benjamin Ebert

Description

Exome sequencing on two independent models of myeloid neoplasms was performed to query off-target effects of Cas9 nuclease. Aligned sequencing data was filtered for reads overlapping predicted off-target cut sites (as determined by algorithm by Hsu et al., 2013) and 161 hematopoiesis and leukemia genes recurrently mutated in hematologic malignancies. Bam files of the filtered sequencing reads for each sample, as well as all of the annotations required for filtering is included.

Files

Steps to reproduce

To create the bed_regions.bed, run: Rscript create_bedfile.R ccds-consensus-coding-sequence-database-grch37-13-_v1-ccds-grch37-13.csv hematopoietic_gene_list.csv predicted_crispr_offtarget_sites.csv bed_regions.bed BAMs were filtered by the bed intervals using samtools: samtools view -L bed_regions.bed -b 1783BM-CD45.sorted.bam > 1783BM-CD45.filtered.bam samtools index 1783BM-CD45.filtered.bam samtools view -L bed_regions.bed -b ZM46BM-CD45.sorted.bam > ZM46BM-CD45.filtered.bam samtools index ZM46BM-CD45.filtered.bam