Theoretical characterisation of strand cross-correlation in ChIP-seq.

ABSTRACT:

Background

Strand cross-correlation profiles are used for both peak calling pre-analysis and quality control (QC) in chromatin immunoprecipitation followed by sequencing (ChIP-seq) analysis. Despite its potential for robust and accurate assessments of signal-to-noise ratio (S/N) because of its peak calling independence, it remains unclear what aspects of quality such strand cross-correlation profiles actually measure.

Results

We introduced a simple model to simulate the mapped read-density of ChIP-seq and then derived the theoretical maximum and minimum of cross-correlation coefficients between strands. The results suggest that the maximum coefficient of typical ChIP-seq samples is directly proportional to the number of total mapped reads and the square of the ratio of signa

SUBMITTER: Anzawa H 

PROVIDER: S-EPMC7510163 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature