KAS-pipe2: a flexible toolkit for exploring KAS-seq and spKAS-seq data

Lyu, R.; Wu, T.; Park, G.; He, Y.; He, C.; Chen, M.

doi:10.1101/2022.08.10.503490

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bioRxiv · 10.1101/2022.08.10.503490

KAS-pipe2: a flexible toolkit for exploring KAS-seq and spKAS-seq data

Lyu, R.·Wu, T.·Park, G.·He, Y.·He, C.·Chen, M.

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Abstract

Kethoxal-assisted ssDNA sequencing (KAS-seq) is gaining popularity as a robust and effective approach to study the dynamics of transcriptionally engaged RNA polymerases through profiling of genome-wide single-stranded DNA (ssDNA). Its latest variant, spKAS-seq, a strand-specific version of KAS-seq, has been developed to map genome-wide R-loop structures by detecting imbalances of ssDNA on two strands. However, user-friendly, open-source analysis pipelines for KAS-seq data are still lacking. Here we present KAS-pipe2 as a flexible and integrated toolkit to facilitate the analysis and interpretation of KAS-seq data. KAS-pipe2 can perform standard analyses such as quality control, read alignment, and differential RNA polymerase activity analysis. In addition, KAS-pipe2 introduces many novel features, including, but not limited to: calculation of transcriptional indexes, identification of single-stranded transcribing enhancers, and high-resolution mapping of R-loops. We use benchmark datasets to demonstrate that KAS-pipe2 provides a powerful framework to study transient transcriptional regulatory programs. KAS-pipe2 is available at https://github.com/Ruitulyu/KAS-pipe2.

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Lyu, R., Wu, T., Park, G., He, Y., He, C., Chen, M.. 2022-08-13. KAS-pipe2: a flexible toolkit for exploring KAS-seq and spKAS-seq data. https://doi.org/10.1101/2022.08.10.503490

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