@article {Babaian149864, author = {Artem Babaian and Richard Thompson and Jake Lever and Liane Gagnier and Mohammad M. Karimi and Dixie L. Mager}, title = {LIONS: Analysis Suite for Detecting and Quantifying Transposable Element Initiated Transcription from RNA-seq}, elocation-id = {149864}, year = {2018}, doi = {10.1101/149864}, publisher = {Cold Spring Harbor Laboratory}, abstract = {Summary Transposable Elements (TEs) influence the evolution of novel transcriptional networks yet the specific and meaningful interpretation of how TE-initiation events contribute to the transcriptome has been marred by computational and methodological deficiencies. We developed LIONS for the analysis of paired-end RNA-seq data to specifically detect and quantify TE-initiated transcripts.Availability Source code, container, test data and instruction manual are freely available at www.github.com/ababaian/LIONS.Contact ababaian{at}bccrc.ca or mahdi.karimi{at}lms.mrc.ac.uk or dmager{at}bccrc.ca.Supplementary information Supplementary data are available at Bioinformatics online.}, URL = {https://www.biorxiv.org/content/early/2018/08/30/149864}, eprint = {https://www.biorxiv.org/content/early/2018/08/30/149864.full.pdf}, journal = {bioRxiv} }