title: tDRmapper: challenges and solutions to mapping, naming, and quantifying tRNA-derived RNAs from human small RNA-sequencing data.
abstract: BACKGROUND
  Small RNA-sequencing has revealed the diversity and high abundance of small RNAs derived from tRNAs, referred to as tRNA-derived RNAs. However, at present, there is no standardized nomenclature and there are no methods for accurate annotation and quantification of these small RNAs. tRNA-derived RNAs have unique features that limit the utility of conventional alignment tools and quantification methods.
  
  
  RESULTS
  We describe here the challenges of mapping, naming, and quantifying tRNA-derived RNAs and present a novel method that addresses them, called tDRmapper. We then use tDRmapper to perform a comparative analysis of tRNA-derived RNA profiles across different human cell types and diseases. We found that (1) tRNA-derived RNA profiles can differ dramatically across different cell types and disease states, (2) that positions and types of chemical modifications of tRNA-derived RNAs vary by cell type and disease, and (3) that entirely different tRNA-derived RNA species can be produced from the same parental tRNA depending on the cell type.
  
  
  CONCLUSIONS
  tDRmappernot only provides a standardized nomenclature and quantification scheme, but also includes graphical visualization that facilitates the discovery of novel tRNA and tRNA-derived RNA biology.
authors.affiliation: Bioinformatics and Computational Biology Curriculum, University of North Carolina, Chapel Hill, NC, USA. SaraRSelitsky@gmail.com.|Departments of Genetics, University of North Carolina, Chapel Hill, NC, USA. SaraRSelitsky@gmail.com.|Microbiology & Immunology, University of North Carolina, Chapel Hill, NC, USA. SaraRSelitsky@gmail.com.
authors.forename: Sara R
authors.initials: SR
authors.lastname: Selitsky
authors.affiliation: Bioinformatics and Computational Biology Curriculum, University of North Carolina, Chapel Hill, NC, USA. praveen_sethupathy@med.unc.edu.|Departments of Genetics, University of North Carolina, Chapel Hill, NC, USA. praveen_sethupathy@med.unc.edu.|Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA. praveen_sethupathy@med.unc.edu.
authors.forename: Praveen
authors.initials: P
authors.lastname: Sethupathy
mesh_terms: D001483:Base Sequence; D002454:Cell Differentiation; D030561:Databases, Nucleic Acid; D006801:Humans; D035683:MicroRNAs / Q000235:genetics*; D008969:Molecular Sequence Data; D009928:Organ Specificity; D012322:RNA Precursors / Q000235:genetics; D012343:RNA, Transfer / Q000235:genetics*; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
chemical_list: D035683:MicroRNAs; D012322:RNA Precursors; D012343:RNA, Transfer