MACS2 安装与使用

时间:2022-04-23 01:42:41
1)下载MACS2
  $ python setup.py install
出现如下问题:
 MACS2/cProb.c -o error: #error Do not use this file, it is the result of a failed Cython compilation.
 error: command 'gcc' failed with exit status 1.
后来更新了gcc(见我的日志 《Ubuntu安装与更新GCC》),安装了gcc4.7.0,同样运行了1),结果同样!(由于MACS2对一些软件的配置版本比较新,所以我对可能需要的用到的东西都进行了升级,换言之,也许更新gcc4.7.0并不能解决问题)
在网上查到一个资料,说需要的Cython版本应该>=0.14.1(https://github.com/taoliu/MACS/issues/3)。

2)安装Cython
在网上下载Cython0.16,运行命令行:
 $ sudo apy-get install python-dev
 $ cd Cython-0.16/
 $ sudo python setup.py install

3) 安装 MACS2
 $ cd MACS-2.0.9
 $ sudo python setup.py install

4) 使用MACS2
macs2 [-h] [--version]
{callpeak,filterdup,bdgpeakcall,bdgcmp,randsample,bdgdiff,bdgbroadcall}
Example for regular peak calling:
  python2.7 macs2 callpeak -t ChIP.bam -c Control.bam -f BAM -g hs -n fileprefix -B -q 0.01
Example for broad peak calling:
  python2.7 macs2 callpeak -t ChIP.bam -c Control.bam --broad -g hs --broad-cutoff 0.1

There are seven major functions available in MACS serving as sub-commands.

callpeak: Main MACS2 Function to Call peaks from alignment results.
bdgpeakcall: Call peaks from bedGraph output.
bdgbroadcall: Call broad peaks from bedGraph output.
bdgcmp: Deduct noise by comparing two signal tracks in bedGraph.
bdgdiff: Differential peak detection based on paired four bedgraph files.
filterdup: Remove duplicate reads at the same position, then convert acceptable format to BED format.
predictd: Predict d or fragment size from alignment results.
pileup: Pileup aligned reads with a given extension size (fragment size or d in MACS language). Note there will be no step for duplicate reads filtering or sequencing depth scaling, so you may need to do certain post- processing.
randsample: Randomly sample number/percentage of total reads.
refinepeak: (Experimental) Take raw reads alignment, refine peak summits and give scores measuring balance of forward- backward tags. Inspired by SPP.

详细参数说明:

https://pypi.python.org/pypi/MACS2 (有下载网址和安装、使用示例)

REF

http://lwzhanghz.blog.163.com/blog/static/136826369201251783236887/