Evaluation of different reference based annotation strategies using RNA-Seq - a case study in Drososphila pseudoobscura.

ABSTRACT: RNA-Seq is a powerful tool for the annotation of genomes, in particular for the identification of isoforms and UTRs. Nevertheless, several software tools exist and no standard strategy to obtain a reliable annotation is yet established. We tested different combinations of the most commonly used reference-based alignment tools (TopHat, GSNAP) in combination with two frequently used reference-based assemblers (Cufflinks, Scripture) and evaluated the potential of RNA-Seq to improve the annotation of Drosophila pseudoobscura. While GSNAP maps a higher proportion of reads, TopHat resulted in a more accurate annotation when used in combination with Cufflinks. Scripture had the lowest sensitivity. Interestingly, after subsampling to the same coverage for GSNAP and TopHat, we find that both mapper

SUBMITTER: Palmieri N 

PROVIDER: S-EPMC3463616 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature