This is a tool that identifies/separates transcripts with intron-retentions from an assembly.
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
Given the input transcript file (in gtf format), irtool will produce two files (in gtf format):
- transcripts with intron-retentions,
- 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 |