MACS2 安装与使用

时间：2016-12-25 09:39:19 收藏：0 阅读：6773

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/