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.zip
mkdir -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 bwa
http://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 --help
Example 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
#https://mp.weixin.qq.com/s?__biz=MzAxMDkxODM1Ng==&mid=2247484370&idx=1&sn=3e29df3b621076bd1d33a8ec157858e5&scene=21#wechat_redirect