PSIM : pattern-based read simulator for RNA-seq analysis

Cited 0 time in scopus
Metadata Downloads
Title
PSIM : pattern-based read simulator for RNA-seq analysis
Author(s)
S M Lee; H Tak; Kiejung Park; H G Cho; D H Lee
Bibliographic Citation
Multimedia Tools and Applications, vol. 74, no. 16, pp. 6465-6480
Publication Year
2015
Abstract
Next-generation sequencing technologies (NGS) require mapping tools that are fundamental for their application. These are evaluated by the level of accuracy to be matched and read at the original location. Evaluation increases the need for a simulator to generate reads with their locations and errors, as with indel. In this paper, we propose a simulator, PSIM, that generating a set of artificial RNA segments(reads) with the expression level and errors based on a pattern-based SAM file. PSIM adopts the contour line transpose and interval section shuffle methods to generate a similar expression level. In addition, we show the similarity between a profile contour of synthesized data and a reference sequence.
Keyword
BioinformaticsRead simulatorRNA-seq
ISSN
1380-7501
Publisher
Springer
DOI
http://dx.doi.org/10.1007/s11042-014-2108-x
Type
Article
Appears in Collections:
1. Journal Articles > Journal Articles
Files in This Item:
  • There are no files associated with this item.


Items in OpenAccess@KRIBB are protected by copyright, with all rights reserved, unless otherwise indicated.