title: Threshold-seq: a tool for determining the threshold in short RNA-seq datasets.
abstract: CONCLUSIONS
  We present 'Threshold-seq,' a new approach for determining thresholds in deep-sequencing datasets of short RNA transcripts. Threshold-seq addresses the critical question of how many reads need to support a short RNA molecule in a given dataset before it can be considered different from 'background.' The proposed scheme is easy to implement and incorporate into existing pipelines.
  
  
  METHODS
  Source code of Threshold-seq is freely available as an R package at: http://cm.jefferson.edu/threshold-seq/.
  
  
  BACKGROUND
  isidore.rigoutsos@jefferson.edu.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA 19107, USA.
authors.forename: Rogan
authors.initials: R
authors.lastname: Magee
authors.affiliation: Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA 19107, USA.
authors.forename: Phillipe
authors.initials: P
authors.lastname: Loher
authors.affiliation: Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA 19107, USA.
authors.forename: Eric
authors.initials: E
authors.lastname: Londin
authors.affiliation: Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA 19107, USA.
authors.forename: Isidore
authors.initials: I
authors.lastname: Rigoutsos
mesh_terms: D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software