| Autor: |
Myles Brown, Nikolas Kesten, Ariel Feiglin, Avery S. Feit, Paloma Cejas, Yingtian Xie, Ningxuan Zhou, Henry W. Long, X. Shirley Liu, Len Taing, Rinath Jeselsohn, Shengqing Gu, Xintao Qiu, Joseph Perkins, Yihao Li |
| Rok vydání: |
2020 |
| Předmět: |
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| DOI: |
10.1101/2020.11.06.367409 |
| Popis: |
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.Code availability: https://bitbucket.org/cfce/cobra |
| Databáze: |
OpenAIRE |
| Externí odkaz: |
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