RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome.

ABSTRACT:

Background

RNA-Seq is revolutionizing the way transcript abundances are measured. A key challenge in transcript quantification from RNA-Seq data is the handling of reads that map to multiple genes or isoforms. This issue is particularly important for quantification with de novo transcriptome assemblies in the absence of sequenced genomes, as it is difficult to determine which transcripts are isoforms of the same gene. A second significant issue is the design of RNA-Seq experiments, in terms of the number of reads, read length, and whether reads come from one or both ends of cDNA fragments.

Results

We present RSEM, an user-friendly software package for quantifying gene and isoform abundances from single-end or paired-end RNA-Seq data. RSEM outputs abundance estimates, 95% cre

SUBMITTER: Li B 

PROVIDER: S-EPMC3163565 | biostudies-literature | 2011 Aug

REPOSITORIES: biostudies-literature