PERTRAN: Genome-guided RNA-seq Read Assembler

Conference · Mon Oct 28 00:00:00 EDT 2013

OSTI ID:1241180

Shu, Shengqiang; Goodstein, David; Rokhsar, Dan

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.

• Research Organization: Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
• Sponsoring Organization: USDOE Office of Science (SC)
• DOE Contract Number: DE-AC02-05CH11231
• OSTI ID: 1241180
• Report Number(s): LBNL-7081E
• Resource Relation: Conference: Cold Spring Harbor Lab Genome Informatics, Cold Spring Harbor, New York, Oct 30 - Nov 2, 2013
• Country of Publication: United States
• Language: English

Related Subjects

99 GENERAL AND MISCELLANEOUS
Short RNA-Seq Reads
PERTRAN
fused-exons
TOPHAT