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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.

SUBMITTER: Magee R 

PROVIDER: S-EPMC5870860 | biostudies-other | 2017 Jul

REPOSITORIES: biostudies-other

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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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