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bioRxiv · 10.1101/2020.03.05.977801

Analyzing and interpreting DNA double-strand break sequencing data

Mitra, A.·Dojer, N.·Fongang, B.·Nde, J.·Zhu, Y.·Rowicka, M.
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Abstract

DNA double-strand breaks (DSBs), are a major threat to genomic stability and may lead to cancer. Several technologies to accurately detect DSBs genome-wide have been developed recently, but still lacking publicly available tools for analysis of the resulting data. Here, we present a step-by-step iSeq package (http://breakome.utmb.edu/software.html), custom designed for analysis and interpretation of DSB-sequencing data. iSeq performs barcode trimming and read counting, and identifies DSB-enriched regions by statistical test and annotate them to the desired genomic features. Applying this package, users can identify and annotate DSB-enriched regions from base pair (eg. Cas9 cleavage sites) up to megabase (eg. DNA replication stress-induced) resolution, and if possible quantify DSB frequencies per cell genome-wide by combining with qDSB-Seq. iSeq can be used for any sequencing-based DSB detection techniques. The analysis for Steps 1-19 can be performed within ~4 hours.

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Mitra, A., Dojer, N., Fongang, B., Nde, J., Zhu, Y., Rowicka, M.. 2020-03-06. Analyzing and interpreting DNA double-strand break sequencing data. https://doi.org/10.1101/2020.03.05.977801

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