Improving CLIP-seq data analysis by incorporating transcript information.

ABSTRACT:

Background

Current peak callers for identifying RNA-binding protein (RBP) binding sites from CLIP-seq data take into account genomic read profiles, but they ignore the underlying transcript information, that is information regarding splicing events. So far, there are no studies available that closer observe this issue.

Results

Here we show that current peak callers are susceptible to false peak calling near exon borders. We quantify its extent in publicly available datasets, which turns out to be substantial. By providing a tool called CLIPcontext for automatic transcript and genomic context sequence extraction, we further demonstrate that context choice affects the performances of RBP binding site prediction tools. Moreover, we show that known motifs of exon-binding RBPs ar

SUBMITTER: Uhl M 

PROVIDER: S-EPMC7745353 | biostudies-literature | 2020 Dec

REPOSITORIES: biostudies-literature