5 years ago

CAM: A quality control pipeline for MNase-seq data

Sheng’en Hu, Yong Zhang, Xiaolan Chen, Ji Liao, Chengchen Zhao, Yiqing Chen

by Sheng’en Hu, Xiaolan Chen, Ji Liao, Yiqing Chen, Chengchen Zhao, Yong Zhang

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/~zhanglab/CAM.

Publisher URL: http://journals.plos.org/plosone/article

DOI: 10.1371/journal.pone.0182771

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