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

Researchers from Thomas Jefferson University 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.

Comparison of Threshold-seq with arbitrary RPM thresholds


The shown five samples were sequenced in seven technical replicates. In each case, we plot the obtained sensitivity (X-axis) vs. the obtained specificity (Y-axis) for different RPMM thresholds from 0.5 to 5 in increments of 0.5. Dark circles show the Threshold-seq equivalent metrics in each case.

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

Magee R, Loher P, Londin E, Rigoutsos I. (2017) Threshold-seq: a tool for determining the threshold in short RNA-seq datasets. Bioinformatics [Epub ahead of print]. [article]

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