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

Summary Detecting intron retention (IR) events is emerging as a specialized need for RNA-seq data analysis. Here we present iREAD ( i ntron RE tention A nalysis and D etector), 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 www.libpls.net/iread Contact [email protected]