CoBRA: Containerized Bioinformatics workflow for Reproducible ChIP/ATAC-seq Analysis - from differential peak calling to pathway analysis

Qiu, X.; Feit, A.; Feiglin, A.; Xie, Y.; Kesten, N.; Taing, L.; Perkins, J.; Zhou, N.; Gu, S.; Li, Y.; Cejas, P.; Jeselsohn, R.; Brown, M.; Liu, X. S.; Long, H. W.

doi:10.1101/2020.11.06.367409

bioRxiv · 10.1101/2020.11.06.367409

CoBRA: Containerized Bioinformatics workflow for Reproducible ChIP/ATAC-seq Analysis - from differential peak calling to pathway analysis

Qiu, X.·Feit, A.·Feiglin, A.·Xie, Y.·Kesten, N.·Taing, L.·Perkins, J.·Zhou, N.·Gu, S.·Li, Y.·Cejas, P.·Jeselsohn, R.·Brown, M.·Liu, X. S.·Long, H. W.

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Abstract

ChIP-seq and ATAC-seq have become essential technologies used as effective methods of measuring protein-DNA interactions and chromatin accessibility. However, there is a need for a scalable and reproducible pipeline that incorporates correct normalization between samples, adjustment of copy number variations, and integration of new downstream analysis tools. Here we present CoBRA, a modularized computational workflow which quantifies ChIP and ATAC-seq peak regions and performs unsupervised and supervised analysis. CoBRA provides a comprehensive state-of-the-art ChIP and ATAC-seq analysis pipeline that is usable by scientists with limited computational experience. This enables researchers to gain rapid insight into protein-DNA interactions and chromatin accessibility through sample clustering, differential peak calling, motif enrichment, comparison of sites to a reference DB and pathway analysis. Code availability: https://bitbucket.org/cfce/cobra

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Qiu, X., Feit, A., Feiglin, A., Xie, Y., Kesten, N., Taing, L., Perkins, J., Zhou, N., Gu, S., Li, Y., Cejas, P., Jeselsohn, R., Brown, M., Liu, X. S., Long, H. W.. 2020-11-08. CoBRA: Containerized Bioinformatics workflow for Reproducible ChIP/ATAC-seq Analysis - from differential peak calling to pathway analysis. https://doi.org/10.1101/2020.11.06.367409

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