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Fig. 5 | BMC Genomics

Fig. 5

From: Q-nexus: a comprehensive and efficient analysis pipeline designed for ChIP-nexus

Fig. 5

ChIP-nexus peak calling (a) Idealized example of a ChIP-nexus peak. The protein of interest (green) is bound via one cross-link to the DNA. The 5’ ends are trimmed by exonuclease (’Pac-Man’ symbols) up to the cross-link position. 5’ end positions of mapped reads, depicted by red and blue arrows, are transformed to a qfrags coverage profile (purple) along the genome. Local maxima within the qfrag coverage are taken as summits. For each summit position s i the number of 5’ end positions within a range of q max is determined and tested for statistical significance. b Comparison of 5’ end and qfrags coverage profiles for Dorsal and Twist. 5’ end (red and blue) and qfrags (purple) coverage profiles at the rho NEE enhancer for Dorsal and Twist (taken from IGV [29]). This region is also shown in the original ChIP-nexus publication [11]. Regions surrounded by clusters of 5’ends on the forward and reverse strand are selectively emphasized by the qfrag method. The qfrags coverage profiles demonstrate two clearly separated peaks for Dorsal and Twist

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