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.
Genomics Proteomics Bioinformatics. 2021 Aug;19(4):652-661. doi: 10.1016/j.gpb.2020.11.007. Epub 2021 Jul 18.
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.
染色质免疫沉淀测序（ChIP-seq）和转座酶可及染色质的高通量测序（ATAC-seq）已成为有效测量蛋白质-DNA 相互作用和染色质可及性的重要技术。然而，需要一个可扩展且可重复的管道，该管道在样本之间进行适当的归一化，校正拷贝数变异，并整合新的下游分析工具。在这里，我们提出了用于可重复 ChIP/ATAC-seq 分析的容器化生物信息学工作流程（CoBRA），这是一个模块化的计算工作流程，可量化 ChIP-seq 和 ATAC-seq 的峰区，并进行无监督和监督分析。CoBRA 提供了一个全面的最先进的 ChIP-seq 和 ATAC-seq 分析管道，具有有限计算经验的科学家也可以使用。这使研究人员能够通过样本聚类、差异峰调用、基序富集、将位点与参考数据库进行比较以及通路分析，快速洞察蛋白质-DNA 相互作用和染色质可及性。CoBRA 可在 https://bitbucket.org/cfce/cobra 上公开获得。
