Supersplat--spliced RNA-seq alignment.

ABSTRACT:

Motivation

High-throughput sequencing technologies have recently made deep interrogation of expressed transcript sequences practical, both economically and temporally. Identification of intron/exon boundaries is an essential part of genome annotation, yet remains a challenge. Here, we present supersplat, a method for unbiased splice-junction discovery through empirical RNA-seq data.

Results

Using a genomic reference and RNA-seq high-throughput sequencing datasets, supersplat empirically identifies potential splice junctions at a rate of approximately 11.4 million reads per hour. We further benchmark the performance of the algorithm by mapping Illumina RNA-seq reads to identify introns in the genome of the reference dicot plant Arabidopsis thaliana and we demonstrate the util

SUBMITTER: Bryant DW 

PROVIDER: S-EPMC2881391 | biostudies-literature | 2010 Jun

REPOSITORIES: biostudies-literature