title: TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets.
abstract: BACKGROUND
  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 and 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.
  
  
  METHODS
  The source code, associated GTF files for TE annotation, and testing data are freely available at http://hammelllab.labsites.cshl.edu/software.
  
  
  BACKGROUND
  mhammell@cshl.edu.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.
authors.forename: Ying
authors.initials: Y
authors.lastname: Jin
authors.affiliation: Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.
authors.forename: Oliver H
authors.initials: OH
authors.lastname: Tam
authors.affiliation: Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.
authors.forename: Eric
authors.initials: E
authors.lastname: Paniagua
authors.affiliation: Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.
authors.forename: Molly
authors.initials: M
authors.lastname: Hammell
mesh_terms: D000818:Animals; D004251:DNA Transposable Elements / Q000235:genetics*; D030541:Databases, Genetic; D004331:Drosophila melanogaster / Q000235:genetics; D020869:Gene Expression Profiling; D051379:Mice; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
chemical_list: D004251:DNA Transposable Elements; D012333:RNA, Messenger