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

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