%0 Journal Article %A Hong-Dong Li %A Cory C. Funk %A Nathan D. Price %T iREAD: A Tool for Intron Retention Detection from RNA-seq Data %D 2017 %R 10.1101/135624 %J bioRxiv %P 135624 %X 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/ireadContact Nathan.Price{at}systemsbiology.org %U https://www.biorxiv.org/content/biorxiv/early/2017/05/09/135624.full.pdf