OccuPeak: ChIP-Seq peak calling based on internal background modelling.

ABSTRACT:

Unlabelled

ChIP-seq has become a major tool for the genome-wide identification of transcription factor binding or histone modification sites. Most peak-calling algorithms require input control datasets to model the occurrence of background reads to account for local sequencing and GC bias. However, the GC-content of reads in Input-seq datasets deviates significantly from that in ChIP-seq datasets. Moreover, we observed that a commonly used peak calling program performed equally well when the use of a simulated uniform background set was compared to an Input-seq dataset. This contradicts the assumption that input control datasets are necessary to fatefully reflect the background read distribution. Because the GC-content of the abundant single reads in ChIP-seq datasets is similar to

SUBMITTER: de Boer BA 

PROVIDER: S-EPMC4061025 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature