博文的顺序有点乱，因为怕读到前面的公共测序数据下载这篇文章的朋友搞不清楚，我如何调用各种软件的，所以我这里强势插入一篇博客来描述这件事，当然也只是略过，我所有的软件理论上都是安装在我的home目录下的biosoft文件夹，所以你看到我一般安装程序都是:
cd ~/biosoft
mkdir macs2 && cd macs2 ##指定的软件安装在指定文件夹里面
这只是我个人的安装习惯，因为我不是root，所以不能在linux系统下做太多事，我这里贴出我所有的软件安装代码：
## pre-step: download sratoolkit /fastx_toolkit_0.0.13/fastqc/bowtie2/bwa/MACS2/HOMER/QuEST/mm9/hg19/bedtools
## http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software
## http://www.ncbi.nlm.nih.gov/books/NBK158900/## Download and install sratoolkit
cd ~/biosoft
mkdir sratoolkit && cd sratoolkit
wget http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.6.3/sratoolkit.2.6.3-centos_linux64.tar.gz
##
## Length: 63453761 (61M) [application/x-gzip]
## Saving to: "sratoolkit.2.6.3-centos_linux64.tar.gz"
tar zxvf sratoolkit.2.6.3-centos_linux64.tar.gz## Download and install bedtools
cd ~/biosoft
mkdir bedtools && cd bedtools
wget https://github.com/arq5x/bedtools2/releases/download/v2.25.0/bedtools-2.25.0.tar.gz
## Length: 19581105 (19M) [application/octet-stream]
tar -zxvf bedtools-2.25.0.tar.gz
cd bedtools2
make## Download and install PeakRanger
cd ~/biosoft
mkdir PeakRanger && cd PeakRanger
wget https://sourceforge.net/projects/ranger/files/PeakRanger-1.18-Linux-x86_64.zip/
## Length: 1517587 (1.4M) [application/octet-stream]
unzip PeakRanger-1.18-Linux-x86_64.zip
~/biosoft/PeakRanger/bin/peakranger -h## Download and install bowtie
cd ~/biosoft
mkdir bowtie && cd bowtie
wget https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.2.9/bowtie2-2.2.9-linux-x86_64.zip/download
#Length: 27073243 (26M) [application/octet-stream]
#Saving to: "download" ## I made a mistake here for downloading the bowtie2
mv download bowtie2-2.2.9-linux-x86_64.zip
unzip bowtie2-2.2.9-linux-x86_64.zipmkdir -p ~/biosoft/bowtie/hg19_index
cd ~/biosoft/bowtie/hg19_index# download hg19 chromosome fasta files
wget http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/chromFa.tar.gz
# unzip and concatenate chromosome and contig fasta files
tar zvfx chromFa.tar.gz
cat *.fa > hg19.fa
rm chr*.fa
## ~/biosoft/bowtie/bowtie2-2.2.9/bowtie2-build ~/biosoft/bowtie/hg19_index/hg19.fa ~/biosoft/bowtie/hg19_index/hg19
## Download and install BWA
cd ~/biosoft
mkdir bwa && cd bwahttp://sourceforge.net/projects/bio-bwa/files/
tar xvfj bwa-0.7.12.tar.bz2 # x extracts, v is verbose (details of what it is doing), f skips prompting for each individual file, and j tells it to unzip .bz2 files
cd bwa-0.7.12
make
export PATH=$PATH:/path/to/bwa-0.7.12 # Add bwa to your PATH by editing ~/.bashrc file (or .bash_profile or .profile file)
# /path/to/ is an placeholder. Replace with real path to BWA on your machine
source ~/.bashrc
# bwa index [-a bwtsw|is] index_prefix reference.fasta
bwa index -p hg19bwaidx -a bwtsw ~/biosoft/bowtie/hg19_index/hg19.fa
# -p index name (change this to whatever you want)
# -a index algorithm (bwtsw for long genomes and is for short genomes)
## Download and install macs2
## // https://pypi.python.org/pypi/MACS2/
cd ~/biosoft
mkdir macs2 && cd macs2
wget ~~~~~~~~~~~~~~~~~~~~~~MACS2-2.1.1.20160309.tar.gz
tar zxvf MACS2-2.1.1.20160309.tar.gz
cd MACS2-2.1.1.20160309
python setup.py install --user#################### The log for installing MACS2:
Creating ~/.local/lib/python2.7/site-packages/site.py
Processing MACS2-2.1.1.20160309-py2.7-linux-x86_64.egg
Copying MACS2-2.1.1.20160309-py2.7-linux-x86_64.egg to ~/.local/lib/python2.7/site-packages
Adding MACS2 2.1.1.20160309 to easy-install.pth file
Installing macs2 script to ~/.local/bin
Finished processing dependencies for MACS2==2.1.1.20160309
############################################################
~/.local/bin/macs2 --helpExample for regular peak calling:
macs2 callpeak -t ChIP.bam -c Control.bam -f BAM -g hs -n test -B -q 0.01
Example for broad peak calling:
macs2 callpeak -t ChIP.bam -c Control.bam --broad -g hs --broad-cutoff 0.1## Download and install homer (Hypergeometric Optimization of Motif EnRichment)
## // http://homer.salk.edu/homer/
## // http://blog.qiubio.com:8080/archives/3024
## pre-install: Ghostscript，seqlogo,blat
cd ~/biosoft
mkdir homer && cd homer
wget http://homer.salk.edu/homer/configureHomer.pl
perl configureHomer.pl -install
perl configureHomer.pl -install hg19
一般来说，对我这样水平的人来说，软件安装就跟家常便饭一样，没有什么问题了，但如果你是初学者呢，肯定没那么轻松，所以请加强学习，我无法在这里讲解太具体的知识了。
所有软件安装完毕后就可以下载文章对这些CHIP-seq的处理结果了，这个很重要，检验我们是否重复了人家的数据分析过程：
## step3 : download the results from paper
## http://www.bio-info-trainee.com/1571.html
mkdir paper_results && cd paper_results
wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE52nnn/GSE52964/suppl/GSE52964_RAW.tar
tar xvf GSE52964_RAW.tarls *gz |xargs gunzip
## step4 : run FastQC to check the sequencing quality.
##这里可以看到我们下载的原始数据已经被作者处理好了，去了接头，去了低质量序列
ls *.fastq | while read id ; do ~/biosoft/fastqc/FastQC/fastqc $id;done
## Sequence length 51
## %GC 39
## Adapter Content passedThe quality of the reads is pretty good, we don't need to do any filter or trim
mkdir QC_results
mv *zip *html QC_results/
所以我们可以直接拿这些数据去做比对了！！！