LIONS: Analysis Suite for Detecting and Quantifying Transposable Element Initiated Transcription from RNA-seq

Abstract

AbstractSummaryTransposable 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.AvailabilitySource code, container, test data and instruction manual are freely available at www.github.com/ababaian/LIONS.Contactababaian@bccrc.ca or mahdi.karimi@lms.mrc.ac.uk or dmager@bccrc.ca.Supplementary informationSupplementary data are available at Bioinformatics online.