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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).