A pipeline to detect and quantify transposable elements (TEs) initiated transcription in paired-end RNA-seq data. The LIONS pipeline uses the following software tools: Python3, pysam, Bowtie2, Tophat2, Java v8 or higher, Samtools v0.1.18, R v3.5.0 or higher, Bedtools v2.25.0, and Cufflinks v2.2.1.
RNA-seq; Gene transcripts; Mobile genetic elements
Babaian A, Thompson IR, Lever J, Gagnier L, Karimi MM, Mager DL "LIONS: analysis suite for detecting and quantifying transposable element initiated transcription from RNA-seq." Bioinformatics. 2019 Oct 1;35(19):3839-3841. https://doi.org/10.1093/bioinformatics/btz130
PMID: 30793157
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