NanoSplicer: accurate identification of splice junctions using Oxford Nanopore sequencing.

ABSTRACT:

Motivation

Long-read sequencing methods have considerable advantages for characterizing RNA isoforms. Oxford Nanopore sequencing records changes in electrical current when nucleic acid traverses through a pore. However, basecalling of this raw signal (known as a squiggle) is error prone, making it challenging to accurately identify splice junctions. Existing strategies include utilizing matched short-read data and/or annotated splice junctions to correct nanopore reads but add expense or limit junctions to known (incomplete) annotations. Therefore, a method that could accurately identify splice junctions solely from nanopore data would have numerous advantages.

Results

We developed 'NanoSplicer' to identify splice junctions using raw nanopore signal (squiggles). For each spl

SUBMITTER: You Y 

PROVIDER: S-EPMC9344838 | biostudies-literature | 2022 Aug

REPOSITORIES: biostudies-literature