Graph Peak Caller: calling ChIP-Seq Peaks on Graph-based Reference Genomes

Graph-based representations are considered to be the future for reference genomes, as they allow integrated representation of the steadily increasing data on individual variation. Currently available tools allow de novo assembly of graph-based reference genomes, alignment of new read sets to the gra...

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Bibliographic Details
Published inbioRxiv
Main Authors Grytten, Ivar, Knut Dagestad Rand, Nederbragt, Alexander J, Storvik, Geir Olve, Glad, Ingrid Kristine, Sandve, Geir Kjetil
Format Paper
LanguageEnglish
Published Cold Spring Harbor Cold Spring Harbor Laboratory Press 06.04.2018
Subjects
Genomes
Graph representations
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Summary:Graph-based representations are considered to be the future for reference genomes, as they allow integrated representation of the steadily increasing data on individual variation. Currently available tools allow de novo assembly of graph-based reference genomes, alignment of new read sets to the graph representation as well as certain analyses like variant-calling and haplotyping. We here present a first method for calling ChIP-Seq peaks on read data aligned to a graph-based reference genome. The method is a graph generalization of the peak caller MACS2 and is implemented in an open source tool, Graph Peak Caller. By using the existing tool vg to build a pan-genome of Arabidopsis thaliana, we validate our approach by showing that Graph Peak Caller with a pan-genome reference graph can trace variants within peaks that are not part of the linear reference genome, and find peaks that in general are more motif-enriched than those found by MACS2.
DOI:10.1101/286823