Allo: Accurate allocation of multi-mapped reads enables regulatory element analysis at repeats.

ABSTRACT: Transposable elements (TEs) and other repetitive regions have been shown to contain gene regulatory elements, including transcription factor binding sites. Unfortunately, regulatory elements harbored by repeats have proven difficult to characterize using short-read sequencing assays such as ChIP-seq or ATAC-seq. Most regulatory genomics analysis pipelines discard "multi-mapped" reads that align equally well to multiple genomic locations. Since multi-mapped reads arise predominantly from repeats, current analysis pipelines fail to detect a substantial portion of regulatory events that occur in repetitive regions. To address this shortcoming, we developed Allo, a new approach to allocate multi-mapped reads in an efficient, accurate, and user-friendly manner. Allo combines probabilistic mappi

SUBMITTER: Morrissey A 

PROVIDER: S-EPMC10515862 | biostudies-literature | 2023 Sep

REPOSITORIES: biostudies-literature