RT Journal Article
SR Electronic
T1 <em>LIONS</em>: Analysis Suite for Detecting and Quantifying Transposable Element Initiated Transcription from RNA-seq
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 149864
DO 10.1101/149864
A1 Artem Babaian
A1 Jake Lever
A1 Liane Gagnier
A1 Dixie L. Mager
YR 2017
UL http://biorxiv.org/content/early/2017/06/13/149864.abstract
AB Transposable Elements (TEs), which comprise almost half of the human genome, can contribute to the evolution of novel transcriptional circuitry. Specific and biologically meaningful interpretation of TE-initiated transcripts has been marred by computational and methodological deficiencies. We developed the software suite LIONS (www.github.com/ababaian/LIONS) to analyze paired-end RNAseq data for detecting and quantifying significant TE-contributions to a transcriptome. The LIONS suite serves as a platform for TE RNA-seq analysis and can be applied to a broad set of data sets for the study of development, stress treatments, aging and cancer.CAGECap Analysis Gene ExpressionERVEndogenous RetrovirusLTRLong Terminal RepeatTETransposable ElementsTSSTranscription Start Site