TEtranscripts: A package for including transposable elements in differential expression analysis of RNA-seq datasets

Jin, Y., Tam, O. H., Paniagua, E., Hammell, M. (2015) TEtranscripts: A package for including transposable elements in differential expression analysis of RNA-seq datasets. Bioinformatics, 31 (22). pp. 3593-3599. ISSN 1367-4811 (Electronic)1367-4803 (Linking)

URL: http://www.ncbi.nlm.nih.gov/pubmed/26206304
DOI: 10.1093/bioinformatics/btv422

Abstract

MOTIVATION: Most RNA-seq data analysis software packages are not designed to handle the complexities involved in properly apportioning short sequencing reads to highly repetitive regions of the genome. These regions are often occupied by transposable elements (TEs), which make up between 20-80% of eukaryotic genomes. They can contribute a substantial portion of transcriptomic and genomic sequence reads, but are typically ignored in most analyses. RESULTS: Here we present a method and software package for including both gene- and TE-associated ambiguously mapped reads in differential expression analysis. Our method shows improved recovery of TE transcripts over other published expression analysis methods, in both synthetic data and qPCR/NanoString-validated published datasets. AVAILABILITY:The source code, associated GTF files for TE annotation, and testing data are freely available at http://hammelllab.labsites.cshl.edu/software. CONTACT:mhammell@cshl.edu.

Item Type: Paper
Subjects: bioinformatics
bioinformatics > genomics and proteomics > computers > computer software
Investigative techniques and equipment > assays > RNA-seq
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > DNA expression > transposable elements
CSHL Authors:
Communities: CSHL labs > Hammell M. lab
Depositing User: Matt Covey
Date Deposited: 27 Jul 2015 19:53
Last Modified: 19 Jun 2017 20:38
PMCID: PMC4757950
Related URLs:
URI: http://repository.cshl.edu/id/eprint/31672

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