Insplico: effective computational tool for studying splicing order of adjacent introns genome-wide with short and long RNA-seq reads.

ABSTRACT: Although splicing occurs largely co-transcriptionally, the order by which introns are removed does not necessarily follow the order in which they are transcribed. Whereas several genomic features are known to influence whether or not an intron is spliced before its downstream neighbor, multiple questions related to adjacent introns' splicing order (AISO) remain unanswered. Here, we present Insplico, the first standalone software for quantifying AISO that works with both short and long read sequencing technologies. We first demonstrate its applicability and effectiveness using simulated reads and by recapitulating previously reported AISO patterns, which unveiled overlooked biases associated with long read sequencing. We next show that AISO around individual exons is remarkably constant acr

SUBMITTER: Gohr A 

PROVIDER: S-EPMC10250204 | biostudies-literature | 2023 Jun

REPOSITORIES: biostudies-literature