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

Abstract

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. Source code of Threshold-seq is freely available as an R package at: http://cm.jefferson.edu/threshold-seq/. isidore.rigoutsos@jefferson.edu. Supplementary data are available at Bioinformatics online.