CoBRA: Containerized Bioinformatics Workflow for Reproducible ChIP/ATAC-seq Analysis |
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| Authors: | Xintao Qiu Avery S Feit Ariel Feiglin Yingtian Xie Nikolas Kesten Len Taing Joseph Perkins Shengqing Gu Yihao Li Paloma Cejas Ningxuan Zhou Rinath Jeselsohn Myles Brown X Shirley Liu Henry W Long |
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| Institution: | Center for Functional Cancer Epigenetics,Dana-Farber Cancer Institute,Boston,MA 02215,USA;Department of Medical Oncology,Dana-Farber Cancer Institute,Harvard Medical School,Boston,MA 02215,USA;Department of Medical Oncology,Dana-Farber Cancer Institute,Harvard Medical School,Boston,MA 02215,USA;Albert Einstein College of Medicine,Bronx,NY 10461,USA;Department of Biomedical Informatics,Harvard Medical School,Boston,MA 02215,USA;Center for Functional Cancer Epigenetics,Dana-Farber Cancer Institute,Boston,MA 02215,USA;Center for Functional Cancer Epigenetics,Dana-Farber Cancer Institute,Boston,MA 02215,USA;Department of Data Sciences,Dana Farber Cancer Institute,Harvard T.H.Chan School of Public Health,Boston,MA 02215,USA;Department of Data Sciences,Dana Farber Cancer Institute,Harvard T.H.Chan School of Public Health,Boston,MA 02215,USA;Department of Medical Oncology,Dana-Farber Cancer Institute,Harvard Medical School,Boston,MA 02215,USA |
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| Abstract: | 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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| Keywords: | ChIP-seq ATAC-seq Snakemake Docker Workflow |
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