Threshold-seq: a tool for determining the threshold in short RNA-seq datasets.
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ABSTRACT: 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: http://cm.jefferson.edu/threshold-seq/.Contact
isidore.rigoutsos@jefferson.edu.Supplementary information
Supplementary data are available at Bioinformatics online.
SUBMITTER: Magee R
PROVIDER: S-EPMC5870860 | biostudies-literature | 2017 Jul
REPOSITORIES: biostudies-literature
Publications
Threshold-seq: a tool for determining the threshold in short RNA-seq datasets.
Magee Rogan R Loher Phillipe P Londin Eric E Rigoutsos Isidore I
Bioinformatics (Oxford, England) 20170701 13
<h4>Summary</h4>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.<h4>Availability and implementation</h4>Source code of Threshold-seq is freely available as an R packa ...[more]
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