LIONS: Analysis suite for detecting and quantifying transposable element initiated transcription from RNA-seq

Abstract

Summary: Transposable elements (TEs) influence the evolution of novel transcriptional networks yet the specific and meaningful interpretation of how TE-derived transcriptional initiation contributes to the transcriptome has been marred by computational and methodological deficiencies. We developed LIONS for the analysis of RNA-seq data to specifically detect and quantify TE-initiated transcripts. Availability and implementation: Source code, container, test data and instruction manual are freely available at www.github.com/ababaian/LIONS. Supplementary information: Supplementary data are available at Bioinformatics online.