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LIONS

LIONS

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.

Topic

RNA-seq; Gene transcripts; Mobile genetic elements

Details

  • Operation: Prediction and recognition
  • Software interface: Command-line user interface
  • Language: Python;Cython
  • Operating system: Linux
  • License: Not stated
  • Cost: Free
  • Version name: -
  • Maturity: Emerging
  • Credit: The Natural Sciences and Engineering Council of Canada (NSERC), University of British Columbia.
  • Contact: Artem Babaian ababaian _at_ bccrc.ca | Mohammad M. Karimi mahdi.karimi _at_ lms.mrc.ac.uk | Dixie L. Mager dmager _at_ bccrc.ca
  • Collection: -

Publications

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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