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

Authors

• Rogan Magee
• Phillipe Loher
• Eric Londin
• Isidore Rigoutsos

Publication/Presentation Date

7-1-2017

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: [email protected].

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Volume

33

Issue

13

First Page

2034

Last Page

2036

ISSN

1367-4811

Published In/Presented At

Magee, R., Loher, P., Londin, E., & Rigoutsos, I. (2017). Threshold-seq: a tool for determining the threshold in short RNA-seq datasets. Bioinformatics (Oxford, England), 33(13), 2034–2036. https://doi.org/10.1093/bioinformatics/btx073

Disciplines

Business Administration, Management, and Operations | Health and Medical Administration | Management Sciences and Quantitative Methods

PubMedID

28203700

Department(s)

Administration and Leadership

Document Type

Article