This is a tool that identifies/separates transcripts with intron-retentions from an assembly.

Installation

Download the source code of the latest release here, then use the following commands to compile:

./configure --prefix=/path/to/your/install/folder
make
make install

Usage

Given the input transcript file (in gtf format), irtool will produce two files (in gtf format):

1. transcripts with intron-retentions,
2. transcripts after filtering out transcripts with intron-retentions.

The usage of irtool is:

irtool <input-gtf-file> <intron-retention-gtf-file> <filtered-gtf-file>

The input-gtf-file is the input transcript file (in gtf format). The intron-retention-gtf-file is an output file (in gtf format) contains all transcripts with intron-retentions. The filtered-gtf-file is another output file (in gtf format) contains the remaining transcripts after filtering.

irtool supports the following parameters.

Parameters	Default Value	Description
-lr	0	minimal overlap length-ratio for partial intron retention identification
-cr	0.5	minimal coverage-ratio
-po	false	turn off partial intron retention identification
-wo	false	turn off entire intron retention identification