SL-quant: a fast and flexible pipeline to quantify spliced leader trans-splicing events from RNA-seq data.

ABSTRACT:

Background

The spliceosomal transfer of a short spliced leader (SL) RNA to an independent pre-mRNA molecule is called SL trans-splicing and is widespread in the nematode Caenorhabditis elegans. While RNA-sequencing (RNA-seq) data contain information on such events, properly documented methods to extract them are lacking.

Findings

To address this, we developed SL-quant, a fast and flexible pipeline that adapts to paired-end and single-end RNA-seq data and accurately quantifies SL trans-splicing events. It is designed to work downstream of read mapping and uses the reads left unmapped as primary input. Briefly, the SL sequences are identified with high specificity and are trimmed from the input reads, which are then remapped on the reference genome and quantified at the nucleo

SUBMITTER: Yague-Sanz C 

PROVIDER: S-EPMC6055573 | biostudies-literature | 2018 Jul

REPOSITORIES: biostudies-literature