ShapeShifter: a novel approach for identifying and quantifying stable lariat intronic species in RNAseq data.

ABSTRACT:

Background

Most intronic lariats are rapidly turned over after splicing. However, new research suggests that some introns may have additional post-splicing functions. Current bioinformatics methods used to identify lariats require a sequencing read that traverses the lariat branchpoint. This method provides precise branchpoint sequence and position information, but is limited in its ability to quantify abundance of stabilized lariat species in a given RNAseq sample. Bioinformatic tools are needed to better address these emerging biological questions.

Methods

We used an unsupervised machine learning approach on sequencing reads from publicly available ENCODE data to learn to identify and quantify lariats based on RNAseq read coverage shape.

Results

We developed ShapeSh

SUBMITTER: Taggart AJ 

PROVIDER: S-EPMC6688498 | biostudies-literature | 2018 Sep

REPOSITORIES: biostudies-literature