CoBRA: Containerized Bioinformatics Workflow for Reproducible ChIP/ATAC-Seq Analysis

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

Subtype heterogeneity and epigenetic convergence in neuroendocrine prostate cancer

“…H3K27ac, ASCL1, and NEUROD1 peaks were called using MACS2 using the same cutoff. DESeq2 was used within the COBRA pipeline 54 to identify differential peaks in ATAC-seq and ChIP-seq, where gained or lost peaks were defined with the threshold of log2-fold change of 1 or 2 and an adjusted p-value < 0.05 54 . PCA was performed using princomp in R.…”

From Reads to Insights: Integrative Pipelines for Biological Interpretation of ATAC-Seq Data

“…In this issue, Liu et al [13] and Qiu et al [14] make great strides toward a standalone analytical ATAC-seq pipeline. Liu et al present the ATAC-seq Integrative Analysis Package (AIAP), which defines a series of ATAC-seq-specific QC metrics to optimize data and further uses a pseudo single-end strategy (PE-asSE) specifically developed for ATAC-seq to improve data analysis [13] .…”

“…In another paper of this issue, Qiu et al present the Containerized Bioinformatics workflow for Reproducible ChIP/ATAC-seq Analysis (CoBRA), which provides a comprehensive and customizable ChIP and ATAC-seq analysis pipeline [14] . The strength of CoBRA is to integrate multiple commonly used functions, including normalization, copy number variation adjustment, sample clustering, differential peak calling, motif enrichment, Cistrome DB Toolkit [15] analysis, and Gene Set Enrichment Analysis (GSEA) [16] pathway analysis into the same package for scientists with limited computational experience.…”

Targeting the BAG-1 family of co-chaperones in lethal prostate cancer

“…ChIP-seq libraries were generated using the ThruPLEX DNA-seq kit (Rubicon Genomics) and were sequenced on the Illumina NextSeq 500 platform at the Molecular Biology Core Facility (Dana-Farber Cancer Institute). All samples were processed through the computational pipeline developed at the Dana-Farber Cancer Institute Center for Functional Cancer Epigenetics (CFCE) using primarily open-source programs (34, 35). Sequence tags were aligned with Burrows-Wheeler Aligner (BWA) to build hg19 and uniquely mapped, non-redundant reads were retained.…”