Threshold-seq: a tool for determining the threshold in short RNA-seq datasets

Bioinformatics. 2017 Jul 1;33(13):2034-2036. doi: 10.1093/bioinformatics/btx073.


Summary: 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.

Availability and implementation: Source code of Threshold-seq is freely available as an R package at:


Supplementary information: Supplementary data are available at Bioinformatics online.

MeSH terms

  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • Sequence Analysis, RNA / methods*
  • Software*