iREAD: A Tool For Intron Retention Detection From RNA-seq Data

Li, H.-D.; Funk, C. C.; Price, N. D.

doi:10.1101/135624

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bioRxiv · 10.1101/135624

iREAD: A Tool For Intron Retention Detection From RNA-seq Data

Li, H.-D.·Funk, C. C.·Price, N. D.

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Abstract

SummaryDetecting 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.\n\nAvailabilitywww.libpls.net/iread\n\nContactNathan.Price@systemsbiology.org

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Li, H.-D., Funk, C. C., Price, N. D.. 2017-05-09. iREAD: A Tool For Intron Retention Detection From RNA-seq Data. https://doi.org/10.1101/135624

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