Hic_breakfinder

简介

a framework that integrates optical mapping, high-throughput chromosome conformation capture (Hi-C), and whole genome sequencing to systematically detect SVs in a variety of normal or cancer samples and cell lines.

可用的版本

版本

平台

构建方式

模块名

1.0

cpu

源码编译

hic_breakfinder/1.0-gcc-9.2.0

数据下载

https://salkinstitute.box.com/s/m8oyv2ypf8o3kcdsybzcmrpg032xnrgx

运行示例

官方提供的数据下载比较慢，作业脚本中 ${Example} 存放了示例数据。

#!/bin/bash
#SBATCH --job-name=hic_breakfinder
#SBATCH --partition=small
#SBATCH --output=%j.out
#SBATCH --error=%j.err
#SBATCH -N 1
#SBATCH --ntasks-per-node=5

module load hic_breakfinder/1.0-gcc-9.2.0
hic_breakfinder --bam-file ${Example}/K562_in_house_b38d5.nodup.bam --exp-file-inter ${Example}/inter_expect_1Mb.hg38.txt --exp-file-intra ${Example}/intra_expect_100kb.hg38.txt --min-1kb --name Out

使用如下脚本提交作业

sbatch test.slurm

运行结果见 Out.breaks.txt

运行资源情况

Cluster: sjtupi
State: COMPLETED (exit code 0)
Nodes: 1
Cores per node: 5
CPU Utilized: 07:57:02
CPU Efficiency: 19.97% of 1-15:48:35 core-walltime
Job Wall-clock time: 07:57:43
Memory Utilized: 4.68 GB
Memory Efficiency: 23.38% of 20.00 GB

小技巧

Hic_breakfinder是单线程的程序，不能有效利用多核资源，建议大家根据内存占用情况来申请资源。

参考资料

最后更新: 2024 年 11 月 19 日