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. 2019 Feb 19;15(2):e1006731. doi: 10.1371/journal.pcbi.1006731

Fig 4. Example of part of a peak detected by Graph Peak Caller and not by MACS2.

Fig 4

Showing part of the graph-based reference genome for A. thaliana on chromosome 1, containing two SNPs (black/blue) and an indel (red) that are not part of the linear reference genome (blue). From the raw ChIP-seq data for the ERF115 transcription factor (NCBI SRA SRR931836) two reads (shown at the top) align perfectly to the graph-based reference genome and Graph Peak Caller is able to detect a peak in this area. Mapping to the linear reference genome does not give sufficiently high mapping score, and so the peak is missed by MACS2.