STRique¶
简介¶
STRique is a python package to analyze repeat expansion and methylation states of short tandem repeats (STR) in Oxford Nanopore Technology (ONT) long read sequencing data.
在 π 集群上安装 STRique¶
首先申请计算节点，然后输入以下指令进行编译：
$ srun -p small -n 4 --pty /bin/bash
$ module load miniconda3/4.7.12.1-gcc-4.8.5
$ conda create -n teststr python=3.6
$ source activate teststr
$ git clone --recursive https://github.com/giesselmann/STRique
$ cd STRique
$ pip install -r requirements.txt
$ python setup.py install
在 π 集群上运行的 Slurm 脚本示例：¶
#!/bin/bash
#SBATCH -J test
#SBATCH -p small
#SBATCH -n 4
#SBATCH --ntasks-per-node=4
#SBATCH -o %j.out
#SBATCH -e %j.err
module load miniconda3/4.7.12.1-gcc-4.8.5
source activate teststr
cd ~/STRique/data
python ../scripts/STRique.py index --recursive c9orf72.fast5 > c9orf72.fofn
cat c9orf72.sam | python ../scripts/STRique.py count c9orf72.fofn ../models/r9_4_450bps.model ../configs/repeat_config.tsv > c9orf72.hg19.strique.tsv
cat c9orf72.hg19.strique.tsv | python ../scripts/STRique.py plot c9orf72.fofn --output c9orf72.pdf --format pdf
参考资料¶
最后更新:
2024 年 11 月 22 日