CHIPIN: ChIP-seq inter-sample normalization based on signal invariance across transcriptionally constant genes.

ABSTRACT:

Background

Multiple studies rely on ChIP-seq experiments to assess the effect of gene modulation and drug treatments on protein binding and chromatin structure. However, most methods commonly used for the normalization of ChIP-seq binding intensity signals across conditions, e.g., the normalization to the same number of reads, either assume a constant signal-to-noise ratio across conditions or base the estimates of correction factors on genomic regions with intrinsically different signals between conditions. Inaccurate normalization of ChIP-seq signal may, in turn, lead to erroneous biological conclusions.

Results

We developed a new R package, CHIPIN, that allows normalizing ChIP-seq signals across different conditions/samples when spike-in information is not available, but

SUBMITTER: Polit L 

PROVIDER: S-EPMC8371782 | biostudies-literature | 2021 Aug

REPOSITORIES: biostudies-literature