PennDiff: detecting differential alternative splicing and transcription by RNA sequencing.

ABSTRACT: Motivation:Alternative splicing and alternative transcription are a major mechanism for generating transcriptome diversity. Differential alternative splicing and transcription (DAST), which describe different usage of transcript isoforms across different conditions, can complement differential expression in characterizing gene regulation. However, the analysis of DAST is challenging because only a small fraction of RNA-seq reads is informative for isoforms. Several methods have been developed to detect exon-based and gene-based DAST, but they suffer from power loss for genes with many isoforms. Results:We present PennDiff, a novel statistical method that makes use of information on gene structures and pre-estimated isoform relative abundances, to detect DAST from RNA-seq data. PennDiff has

SUBMITTER: Hu Y 

PROVIDER: S-EPMC6041879 | biostudies-literature | 2018 Jul

REPOSITORIES: biostudies-literature