Fig. 2
From: iREAD: a tool for intron retention detection from RNA-seq data
Illustration of the usage and output of iREAD. a an example run of iREAD on a mouse RNA-seq data that is included in the package. In addition to the RNA-seq BAM file and the intron file, ‘-o’ and ‘-t’ specify the output directory and the library size, respectively. b example rows of the output file resulting from (a). As shown, this file contains 7 columns. The first column is the intron ID. By default, iREADs uses strict criteria (fragments≥20, junction_reads≥1, FPKM≥3 and entropy_score > =0.9) to filter for intron retention events. The last column indicates whether an intron is retained (‘yes’) or not (‘no’). Note that the threshold for determining intron retention are optional parameters and can be tuned by the users