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CoBRA: Containerized Bioinformatics workflow for Reproducible ChIPATAC-seq Analysis - from differential peak calling to pathway analysis
Link to bioRxiv paper:
http://biorxiv.org/cgi/content/short/2020.11.06.367409v1?rss=1
Authors: 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.
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.
Copy rights belong to original authors. Visit the link for more info
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By Multimodal LLCLink to bioRxiv paper:
http://biorxiv.org/cgi/content/short/2020.11.06.367409v1?rss=1
Authors: 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.
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.
Copy rights belong to original authors. Visit the link for more info