bioRxiv preprint doi: https://doi.org/10.1101/313999; this version posted May 4, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. 1 SQuIRE: Software for Quantifying Interspersed Repeat Elements 2 Authors: Yang Wan R.1, Daniel Ardeljan1,2, Clarissa N. Pacyna 1,3, Lindsay M. Payer1,6, Kathleen H. 3 Burns1,3, 4,5,6 4 1 Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205, 5 USA. 6 2 McKusick-Nathans Institute of Genetics, Johns Hopkins University School of Medicine, Baltimore, 7 Maryland, 21205, USA. 8 3 Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA 9 4 Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA. 10 5 Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, 11 Baltimore, Maryland, USA. 12 6 These authors contributed equally to this work. 13 Running Title: SQuIRE 14 Keywords: TE, retrotransposon, mobile element, RNA-seq alignment, differential expression 15 analysis 16 Corresponding author:Kathleen H. Burns, M.D., Ph.D. 17 Johns Hopkins University School of Medicine 18 733 N. Broadway, MRB 447 19 Baltimore, MD 21205 20
[email protected] 21 410-502-7214 1 bioRxiv preprint doi: https://doi.org/10.1101/313999; this version posted May 4, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.