ASGAL: aligning RNA-Seq data to a splicing graph to detect novel alternative splicing events.

ABSTRACT:

Background

While the reconstruction of transcripts from a sample of RNA-Seq data is a computationally expensive and complicated task, the detection of splicing events from RNA-Seq data and a gene annotation is computationally feasible. This latter task, which is adequate for many transcriptome analyses, is usually achieved by aligning the reads to a reference genome, followed by comparing the alignments with a gene annotation, often implicitly represented by a graph: the splicing graph.

Results

We present ASGAL (Alternative Splicing Graph ALigner): a tool for mapping RNA-Seq data to the splicing graph, with the specific goal of detecting novel splicing events, involving either annotated or unannotated splice sites. ASGAL takes as input the annotated transcripts of a gene and

SUBMITTER: Denti L 

PROVIDER: S-EPMC6247705 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature