IRSim: Simulation of Intron Retention in Coding RNA

Latest version 0.0.3

This software is created to simulate RNA sequencing datasets (Illumina NGS) with pseudo-random intron retention events in coding RNA transcripts. The simulated datasets can be used to evaluate and benchmark intron-retention detection softwares or workflows. IRSim is a software package written in Python3 and employs DWGSIM for NGS read simulation.

The percent intron retention (PIR) of each retained intron is calculated by [100 x mean retention reads divided by the sum of retention reads and spliced intron reads] as seen in Braunschweig et al., 2014.

Installation

Requirements

1. Python 3 (3.6.7 or above)
2. numpy (1.16.2 or above) Link
3. pyfaidx (0.5.5.2 or above) Link
4. DWGSIM (0.1.11 or above) Link

Clone git repository:

git clone https://github.com/cytham/irsim.git 
cd irsim
chmod +x irsim

Quick start

1. Required input files

Make sure you have the following input files ready:

1. A reference genome file in FASTA format
2. cDNA FASTA file
3. Annotation GTF file
4. A tab-delimited FPKM model file (Column 1 - Gene id \t Column 2 - FPKM values)

2. Edit config.ini file

• Add path to DWGSIM directory

DWGSIM directory = /path/to/DWGSIM_directory 

• Edit all other parameters to your choice

Number of threads = 10 
Number of replicates for sample A (Experimental sample) = 1
Number of replicates for sample B (Control sample) = 1
.
.
.

3. Run IRSim

/path/to/irsim ref_genome.fa cDNA.fa annotation.gtf FPKM_model.tsv config.ini output_directory

3. Output files

• Gzipped FASTQ paired-read files for each sample/replicate.
• A report file showing the Percent Intron Retention (PIR) for each intron in each sample/replicate.

Versioning

See Releases

Citation

Author

• Tham Cheng Yong - cytham

License

This project is licensed under GNU General Public License - see LICENSE for details.