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iREAD: A Tool for Intron Retention Detection from RNA-seq Data

Hong-Dong Li, Cory C. Funk, Nathan D. Price
doi: https://doi.org/10.1101/135624
Hong-Dong Li
1School of Information Science and Engineering, Central South University, Changsha, Hunan Province 410083, P.R. China
2Institute for Systems Biology, Seattle, WA 98109, United States
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Cory C. Funk
2Institute for Systems Biology, Seattle, WA 98109, United States
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Nathan D. Price
2Institute for Systems Biology, Seattle, WA 98109, United States
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Abstract

Summary Detecting intron retention (IR) events is emerging as a specialized need for RNA-seq data analysis. Here we present iREAD (intron REtention Analysis and Detector), a tool to detect IR events genome-wide from high-throughput RNA-seq data. The command line interface for iREAD is implemented in Python. iREAD takes as input an existing BAM file, representing the transcriptome, and a text file containing the intron coordinates of a genome. It then 1) counts all reads that overlap intron regions, 2) detects IR vents by analyzing features of reads such as depth and distribution patterns, and 3) outputs a list of retained introns into a tab-delimited text file. The output can be directly used for further exploratory analysis such as differential intron expression and functional enrichment. iREAD provides a new and generic tool to interrogate poly-A enriched transcriptomic data of intron regions.

Availability http://www.libpls.net/iread

Contact Nathan.Price{at}systemsbiology.org

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted May 09, 2017.
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iREAD: A Tool for Intron Retention Detection from RNA-seq Data
Hong-Dong Li, Cory C. Funk, Nathan D. Price
bioRxiv 135624; doi: https://doi.org/10.1101/135624
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iREAD: A Tool for Intron Retention Detection from RNA-seq Data
Hong-Dong Li, Cory C. Funk, Nathan D. Price
bioRxiv 135624; doi: https://doi.org/10.1101/135624

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