Display Settings:

Format

Send to:

Choose Destination
See comment in PubMed Commons below
Biochem Biophys Res Commun. 2011 Jun 3;409(2):299-303. doi: 10.1016/j.bbrc.2011.05.005. Epub 2011 May 7.

Observations on novel splice junctions from RNA sequencing data.

Author information

  • 1College of Computer Science and Technology, Jilin University, Changchun 130012, China.

Abstract

High-throughput RNA sequencing (RNA-seq) technology provides a revolutionary approach to studying splicing events de novo. However, identifying splice junctions with high sensitivity and specificity remains a challenge. In the present study, we proposed a new tool named SeqSaw to detect splice junctions with or without the canonical GT-AG splicing signal. SeqSaw was applied to two ENCODE RNA-seq datasets and also compared with two existing methods. It was shown that the proposed method obtained better results on finding novel splice junctions. Experiments also revealed that the current sequencing depth has not yet reached saturation to detect novel transcripts. Moreover, by comparing the number of supporting reads, we demonstrated that many un-annotated splicing events can be tissue specific.

Copyright © 2011 Elsevier Inc. All rights reserved.

PMID:
21575597
[PubMed - indexed for MEDLINE]
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Icon for Elsevier Science
    Loading ...
    Write to the Help Desk