RNASEQR—a streamlined and accurate RNA-seq sequence analysis program

RNASEQR—a streamlined and accurate RNA-seq sequence analysis program

RNASEQR analyzes raw data from RNA-seq experiments effectively and outputs results in a manner that is compatible with a wide variety of specialized downstream analyses on desktop computers. The RNASEQR method has been systematically compared with four of the most widely used tools (ERANGE, MapSplice , SpliceMap and TopHat),using a simulated data set created from the Consensus CDS project and two experimental RNA-seq data sets generated from a human glioblastoma patient. The results showed that RNASEQR yields more accurate estimates for gene expression, complete gene structures and new transcript isoforms, as well as more accurate detection of single nucleotide variants (SNVs).

RNASEQR and its open source code are available at https://github.com/rnaseqr/RNASEQR.

  • Chen LY, Wei KC, Huang AC, Wang K, Huang CY, Yi D, Tang CY, Galas DJ, Hood LE. (2011) RNASEQR–a streamlined and accurate RNA-seq sequence analysis program. Nucleic Acids Res[Epub ahead of print]. [article]