skip to main content

Title: PERTRAN: Genome-guided RNA-seq Read Assembler

As short RNA-seq reads become a standard, affordable input to any genome annotation project, a sensitive and accurate transcript assembler is an essential part of any gene prediction system. PERTRAN is a pipeline for assembling transcripts from RNA-seq reads which demonstrates higher sensitivity, with fewer fused exons (in most cases), and faster run times compared to other TOPHAT/CUFFLINKS and genome-guided Trinity. PERTRAN shows slightly lower specificity with increased gene fusions in some cases, discussed below. SAM files generated from PERTRAN can be used to compute expression level by cuffdiff and result is comparable to that from TOPHAT.
Authors:
; ;
Publication Date:
OSTI Identifier:
1241180
Report Number(s):
LBNL-7081E
DOE Contract Number:
DE-AC02-05CH11231
Resource Type:
Conference
Resource Relation:
Conference: Cold Spring Harbor Lab Genome Informatics, Cold Spring Harbor, New York, Oct 30 - Nov 2, 2013
Research Org:
Ernest Orlando Lawrence Berkeley National Laboratory, Berkeley, CA (US)
Sponsoring Org:
USDOE Office of Science (SC)
Country of Publication:
United States
Language:
English
Subject:
99 GENERAL AND MISCELLANEOUS Short RNA-Seq Reads, PERTRAN, fused-exons, TOPHAT