Systematic Assessment of RNA-Seq Quantification Tools Using Simulated Sequence Data.

ABSTRACT: RNA-sequencing (RNA-seq) technology has emerged as the preferred method for quantification of gene and isoform expression. Numerous RNA-seq quantification tools have been proposed and developed, bringing us closer to developing expression-based diagnostic tests based on this technology. However, because of the rapidly evolving technologies and algorithms, it is essential to establish a systematic method for evaluating the quality of RNA-seq quantification. We investigate how different RNA-seq experimental designs (i.e., variations in sequencing depth and read length) affect various quantification algorithms (i.e., HTSeq, Cufflinks, and MISO). Using simulated data, we evaluate the quantification tools based on four metrics, namely: (1) total number of usable fragments for quantification, (2

SUBMITTER: Chandramohan R 

PROVIDER: S-EPMC4985018 | biostudies-literature | 2013 Sep

REPOSITORIES: biostudies-literature