RNA Transcriptome Mapping with GraphMap

Next generation sequencing technologies have made RNA sequencing widely accessible and applicable in many areas of research. In recent years, 3rd generation sequencing technologies have matured and are slowly replacing NGS for DNA sequencing. This paper presents a novel tool for RNA mapping guided by gene annotations. The tool is an adapted version of a previously developed DNA mapper - GraphMap, tailored for third generation sequencing data, such as those produced by Pacific Biosciences or Oxford Nanopore Technologies devices. It uses gene annotations to generate a transcriptome, uses a DNA mapping algorithm to map reads to the transcriptome, and finally transforms the mappings back to genome coordinates. Modified version of GraphMap is compared on several synthetic datasets to the state-of-the-art RNAseq mappers enabled to work with third generation sequencing data. The results show that our tool outperforms other tools in general mapping quality.