» A Bioconductor package for identifying off-targets with GUIDE-seq data

(A collaboration with Dr. Wolfe)

The package implements GUIDE-seq analysis workflow in a flexible platform with more than 60 adjustable parameters for the analysis of datasets associated with custom nuclease applications. These parameters allow data analysis to be tailored to different nuclease platforms with different length and complexity in their guide and PAM recognition sequences or their DNA cleavage position. They also enable users to customize sequence aggregation criteria, and vary peak calling thresholds that can influence the number of potential off-target sites recovered. GUIDEseq also annotates potential off-target sites that overlap with genes based on genome annotation information, as these may be the most important off-target sites for further characterization. In addition, GUIDEseq enables the comparison and visualization of off-target site overlap between different datasets for a rapid comparison of different nuclease configurations or experimental conditions.

Zhu LJ, Lawrence M, Gupta A, Pages H, Kucukural A, Garber M, Wolfe SA (2017). “GUIDEseq: A Bioconductor package to analyze GUIDE-Seq datasets for CRISPR-Cas nucleases.” BMC Genomics, 18(1). http://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3746-y.