Journal
PLOS ONE
Volume 12, Issue 8, Pages -Publisher
PUBLIC LIBRARY SCIENCE
DOI: 10.1371/journal.pone.0182771
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Funding
- National Natural Science Foundation of China [31571365, 31322031, 31371288]
- National Key Research and Development Program of China [2017YFA0102602, 2016YFA0100400]
- Specialized Research Fund for the Doctoral Program of Higher Education [20130072110032]
- Program of Shanghai Academic Research Leader [17XD1403600]
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Nucleosome organization affects the accessibility of cis-elements to trans-acting factors. Micrococcal nuclease digestion followed by high-throughput sequencing (MNase-seq) is the most popular technology used to profile nucleosome organization on a genome-wide scale. Evaluating the data quality of MNase-seq data remains challenging, especially in mammalian. There is a strong need for a convenient and comprehensive approach to obtain dedicated quality control (QC) for MNase-seq data analysis. Here we developed CAM, which is a comprehensive QC pipeline for MNase-seq data. The CAM pipeline provides multiple informative QC measurements and nucleosome organization profiles on different potentially functional regions for given MNase-seq data. CAM also includes 268 historical MNase-seq datasets from human and mouse as a reference atlas for unbiased assessment. CAM is freely available at: http://www.tongji.edu.cn/similar to zhanglab/CAM.
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