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MACS2 安装与使用

2024-08-29 05:29:33   214人阅读

 

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

  $ 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/

 

 

 

MACS2 安装与使用


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