Scavenger: A pipeline for recovery of unaligned reads utilising similarity with aligned reads.

ABSTRACT: Read alignment is an important step in RNA-seq analysis as the result of alignment forms the basis for downstream analyses. However, recent studies have shown that published alignment tools have variable mapping sensitivity and do not necessarily align all the reads which should have been aligned, a problem we termed as the false-negative non-alignment problem. Here we present Scavenger, a python-based bioinformatics pipeline for recovering unaligned reads using a novel mechanism in which a putative alignment location is discovered based on sequence similarity between aligned and unaligned reads. We showed that Scavenger could recover unaligned reads in a range of simulated and real RNA-seq datasets, including single-cell RNA-seq data. We found that recovered reads tend to contain more gen

SUBMITTER: Yang A 

PROVIDER: S-EPMC7459848 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature