Assessment of the impact of using a reference transcriptome in mapping short RNA-Seq reads.

ABSTRACT: RNA-Seq has become increasingly popular in transcriptome profiling. The major challenge in RNA-Seq data analysis is the accurate mapping of junction reads to their genomic origins. To detect splicing sites in short reads, many RNA-Seq aligners use reference transcriptome to inform placement of junction reads. However, no systematic evaluation has been performed to assess or quantify the benefits of incorporating reference transcriptome in mapping RNA-Seq reads. In this paper, we have studied the impact of reference transcriptome on mapping RNA-Seq reads, especially on junction ones. The same dataset were analysed with and without RefGene transcriptome, respectively. Then a Perl script was developed to analyse and compare the mapping results. It was found that about 50-55% junction reads ca

SUBMITTER: Zhao S 

PROVIDER: S-EPMC4081564 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature