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Table 1 Number of NFKB peaks from BWA and Novoalign mapped reads

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

Type GM12878_NFKB_IP_rep1 GM12878_NFKB_IP_rep2 GM12891_NFKB_IP_rep1 GM12891_NFKB_IP_rep2
  A B A B A B A B
Overlapped peaks 1512 1513 9942 9960 2257 2264 6082 6082
Unique peaks w/ motif 176 18 409 90 88 19 36 30
Unique peaks w/o motif 134 28 590 249 442 74 21 7
Total peaks 1822 1559 10941 10299 2787 2357 6139 6119
  1. Peaks were identified using MACS (−f BAM -g hs --keep-dup 1 -q 0.01) and motif finding by MEME suite (−dna -mod zoops -nmotifs 5 -minw 10 -maxw 20 -maxsize 999999999 -revcomp). Shown were the number of overlapped peaks between BWA mapped reads (A) and Novoalign mapped reads (B), and number of aligner-specific peaks with or without NFKB binding motif. ChIP-Seq from each cell line had two biological replicates (rep1 and rep2).