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Table 5 Number of ER peaks from MCF-7 cell line

From: HiChIP: a high-throughput pipeline for integrative analysis of ChIP-Seq data

Type IP_1 vs. control IP_2 vs. control IP_3 vs. control
  A B A B A B
Unique reads (million) 16.9 22.27 21.08 22.66 25.36 29.15
Overlapped peaks 62184 62407 41455 41551 54309 54354
Unique peaks 7206 1689 5233 238 3348 857
Unique peaks w/ motif 2552 670 1359 35 1121 362
Unique peaks w/o motif 4654 1019 3874 203 2227 495
Total peaks 69390 64096 46688 41789 57657 55211
  1. Peaks were called by MACS (−f BAM -g hs --keep-dup all -q 0.01) from BWA-mapped reads (to hg18). Motif was identified using MEME as described above. A: number of ER peaks identified by this pipeline, using duplicate-filtered reads (by Picard); B: number of peaks from reads without duplicate removal. IP_1 to IP_3 are three replicates, IP_1: GSM798423, IP_2: GSM798424, IP_3: GSM798425; control (input): GSM798440.
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BMC Bioinformatics

ISSN: 1471-2105

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