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Fig. 2 | BMC Bioinformatics

Fig. 2

From: Systematic evaluation of the impact of ChIP-seq read designs on genome coverage, peak identification, and allele-specific binding detection

Fig. 2

Effect of designs on peak calling. a Number of MAFK peaks by the SPP+IDR pipeline. b Reproducibility of the top SPP peaks of the simulated data. The black solid vertical line is the number of true peaks. c Percentages of the top SPP-identified MAFK peaks with the motif. d–f The 0.3, 0.5, and 0.7 quantiles of the distance between the motifs and the peak summits for the top ranked SPP peaks, MOSAiCS peaks and MACS2 for MAFK, respectively. Their legends are the same as in (c). g–h UCSC Genome browser view over two PE and SE specific BHLHE40 peaks with large coverage change. chr16:68155100 g was identified as a peak only with PE36v1 but not SE36v1, and chr1:145159593 h was identified only with SE75v2 but not PE36v1. The coverage tracks in each peak are normalized to the same scale. Lighter color on the mappability tracks indicates low mappability

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BMC Bioinformatics

ISSN: 1471-2105

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