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ChIP-seq data processing

ML Meng Li
YH Yujie Han
CW Chaochen Wang
WK Wenfeng Kang
WJ Wenyan Jiang
LZ Lei Zhang
YT Yujie Tang
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All ChIP-seq data sets were aligned to the human genome (build version: GRCh38/hg38) using Bowtie 2 (version 2.3.0) [22]. SAM files generated by Bowtie2 were then converted to BAM files with samtools (version 1.9) [23]. Multi-mappers and duplicates were filtered out by sambamba (version 0.7.1) [24]. ChIP-seq peaks over input sample were identified using a peak-finding algorithm, MACS2 (version 2.2.6) [25]. A q value of 0.05 was set as threshold of enrichment for all data sets. Active enhancers were defined as regions of ChIP-seq enrichment for the enhancer-associated histone modification H3K27Ac outside of promoters (excluding the ± 2.5 kb region flanking the promoter). In order to accurately capture dense clusters of enhancers, stitching distance of 12.5 kb was allowed for separate H3K27Ac regions. Super-enhancers were identified and analyzed as described previously [26].

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