PT  - JOURNAL ARTICLE
AU  - Artem Babaian
AU  - Jake Lever
AU  - Liane Gagnier
AU  - Dixie L. Mager
TI  - <em>LIONS</em>: Analysis Suite for Detecting and Quantifying Transposable Element Initiated Transcription from RNA-seq
AID  - 10.1101/149864
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 149864
4099  - http://biorxiv.org/content/early/2017/06/13/149864.short
4100  - http://biorxiv.org/content/early/2017/06/13/149864.full
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