A tool to simulate fasta sequence with m6A peak
- JDK 8
- This tool can be installed by instructions as follows:
git clone https://github.com/canceromics/MeRIP-simulator.git
cd circm6a/m6asimulate/src
javac -d ./ -classpath ./lib/* ./sim/*.java ./genome/*.java ./note/*.java
jar -cvmf META-INF/MANIFEST.MF ../../m6asim.jar *
The tool is generated as m6asim.jar in this directory.
- Start from genome sequence file and annotation file.
java -Xmx8g -jar m6asim.jar -g <genome.fa> -r <annotation.gtf> -p <peak.bed> -m <mutation.bed> -ip <ip.fastq> -in <input.fastq> [options]
Running this instruction will result in getting files named peak.bed, mutation.bed, ip.fastq, input.fastq. You can provide peak.bed, mutation.bed as well.
- Here are definitions of headers in output file named
(output_dir/file_prefix)_circRNAs.txt
| Option | Description |
|---|---|
| -bn | Background number (> 0) for simulation. (10 default) |
| -en | Peak enrichment number (>= 0) for simulation. (15 default) |
| -sl | Read length in pair_end simulation, single-end mode enable when no greater than read length. (200 ~ 450 recommend) (350 default) |
| -rl | Alignment mate length (> 0) in simulation. (150 default) |
| -mrl | Minimum alignment mate length (> 0) in simulation. (5 default) |
| -rs | Random segment size in simulation. Therefore, simulated sequence length between alignment length ¡À random segment size. |
| -mp | Proportion (0.0 ~ 1.0) of mutation reads provided. (0.5 default) |
| -q | Qualities of bases simulated from this |
Licensed GPLv3 for open source use or contact zuoLab (zuozhx@sysucc.org.cn) for commercial use.