1.CoBRA: Containerized Bioinformatics Workflow for Reproducible ChIP/ATAC-seq Analysis
Qiu XINTAO ; S.Feit AVERY ; Feiglin ARIEL ; Xie YINGTIAN ; Kesten NIKOLAS ; Taing LEN ; Perkins JOSEPH ; Gu SHENGQING ; Li YIHAO ; Cejas PALOMA ; Zhou NINGXUAN ; Jeselsohn RINATH ; Brown MYLES ; Liu X.SHIRLEY ; W.Long HENRY
Genomics, Proteomics & Bioinformatics 2021;19(4):652-661
Chromatin immunoprecipitation sequencing (ChIP-seq) and the Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) have become essential technologies to effectively measure protein–DNA interactions and chromatin accessibility. However, there is a need for a scalable and reproducible pipeline that incorporates proper normalization between samples, correction of copy number variations, and integration of new downstream analysis tools. Here we present Containerized Bioinformatics workflow for Reproducible ChIP/ATAC-seq Analysis (CoBRA), a modularized computational workflow which quantifies ChIP-seq and ATAC-seq peak regions and performs unsupervised and supervised analyses. CoBRA provides a comprehensive state-of-the-art ChIP-seq and ATAC-seq analysis pipeline that can be used 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 database, and pathway analysis. CoBRA is publicly available online at https://bitbucket. org/cfce/cobra.
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