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）。
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/