PePr: a peak-calling prioritization pipeline to identify consistent or differential peaks from replicated ChIP-Seq data.

ABSTRACT:

Motivation

ChIP-Seq is the standard method to identify genome-wide DNA-binding sites for transcription factors (TFs) and histone modifications. There is a growing need to analyze experiments with biological replicates, especially for epigenomic experiments where variation among biological samples can be substantial. However, tools that can perform group comparisons are currently lacking.

Results

We present a peak-calling prioritization pipeline (PePr) for identifying consistent or differential binding sites in ChIP-Seq experiments with biological replicates. PePr models read counts across the genome among biological samples with a negative binomial distribution and uses a local variance estimation method, ranking consistent or differential binding sites more favorably than s

SUBMITTER: Zhang Y 

PROVIDER: S-EPMC4155259 | biostudies-literature | 2014 Sep

REPOSITORIES: biostudies-literature