Yanagi: Fast and interpretable segment-based alternative splicing and gene expression analysis.

ABSTRACT:

Background

Ultra-fast pseudo-alignment approaches are the tool of choice in transcript-level RNA sequencing (RNA-seq) analyses. Unfortunately, these methods couple the tasks of pseudo-alignment and transcript quantification. This coupling precludes the direct usage of pseudo-alignment to other expression analyses, including alternative splicing or differential gene expression analysis, without including a non-essential transcript quantification step.

Results

In this paper, we introduce a transcriptome segmentation approach to decouple these two tasks. We propose an efficient algorithm to generate maximal disjoint segments given a transcriptome reference library on which ultra-fast pseudo-alignment can be used to produce per-sample segment counts. We show how to apply these m

SUBMITTER: Gunady MK 

PROVIDER: S-EPMC6693274 | biostudies-literature | 2019 Aug

REPOSITORIES: biostudies-literature