PT  - JOURNAL ARTICLE
AU  - Sheng’en Hu
AU  - Xiaolan Chen
AU  - Ji Liao
AU  - Yiqing Chen
AU  - Chengchen Zhao
AU  - Yong Zhang
TI  - CAM: a quality control pipeline for MNase-seq data
AID  - 10.1101/143263
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 143263
4099  - http://biorxiv.org/content/early/2017/05/28/143263.short
4100  - http://biorxiv.org/content/early/2017/05/28/143263.full
AB  - 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