NGS_data_analysis_pipeline

Shell scripts for analyzing NGS data such as RNA-seq, smallRNA-seq, ChIP-seq, BRIC-seq, PAR-CLIP and ribosome profiling(Ribo-seq).

---

##Requisite Fastqc
Fastx-toolkits
cutadapt
PRINSEQ-lite
Bowtie
Bowtie2
TotHat
Cufflinks
samtools
Bedtools
MACS14
HTSeq(htseq-count)
SRA Toolkit
Trimmomatic
PARalyzer
cERMIT
PhyloGibbs
PhyloGibbs-MP
STAR
RiboTaper
RSEM
BWA
Picard
subread (featureCounts)
circos
fusim

##Install At first, make 'software' directory for installing each software.

mkdir ~/software

---

• Fastqc

wget http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.3.zip
unzip fastqc_v0.11.3.zip
cd FastQC
chmod 755 fastqc
pwd
#~/software/FastQC
echo 'export PATH=~/software/FastQC:${PATH}' >> ~/.bashrc

---

• Fastx-toolkits

wget http://hannonlab.cshl.edu/fastx_toolkit/fastx_toolkit_0.0.13_binaries_Linux_2.6_amd64.tar.bz2
mkdir fastx_toolkit_0_0_13
mv fastx_toolkit_0.0.13_binaries_Linux_2.6_amd64.tar.bz2 fastx_toolkit_0_0_13
cd fastx_toolkit_0_0_13
tar jxvf fastx_toolkit_0.0.13_binaries_Linux_2.6_amd64.tar.bz2
cd bin
pwd
#~/software/fastx_toolkit_0_0_13/bin
echo 'export PATH=~/software/fastx_toolkit_0_0_13/bin:${PATH}' >> ~/.bashrc

---

• PRINSEQ-lite

tar zxvf prinseq-lite-0.20.4.tar.gz
cd prinseq-lite-0.20.4
chmod 755 prinseq-lite.pl
chmod 755 prinseq-graphs.pl
chmod 755 prinseq-graphs-noPCA.pl
pwd
#~/software/prinseq-lite-0.20.4
echo 'export PATH=~/software/prinseq-lite-0.20.4:${PATH}' >> ~/.bashrc

---

• cutadapt

###python_settings###
#Make_directory
mkdir -p ~/software/python_path/lib/python2.7/site-packages/

#.bashrc setting
echo 'export PYTHONHOME=/usr/local' >> ~/.bashrc
echo 'export PYTHONPATH=~/software/python_path/lib/python2.7/site-packages' >> ~/.bashrc
echo 'export PATH=~/software/python_path/bin:${PYTHONHOME}/bin:${PATH}' >> ~/.bashrc
echo 'export LD_LIBRARY_PATH=~/software/python_path/lib:${LD_LIBRARY_PATH}' >> ~/.bashrc

###cutadapt_installation###
wget https://pypi.python.org/packages/source/c/cutadapt/cutadapt-1.8.3.tar.gz#md5=c7384f3bb834375ad8b0a2869827be6f
tar zxvf cutadapt-1.8.3.tar.gz
cd cutadapt-1.8.3
python setup.py build
python setup.py install --prefix=~/software/python_path

---

• Bowtie

unzip bowtie-1.1.2-linux-x86_64.zip
cd bowtie-1.1.2
pwd
#~/software/bowtie-1.1.2
echo 'export PATH=~/software/bowtie-1.1.2:${PATH}' >> ~/.bashrc

---

• Bowtie2

unzip bowtie2-2.2.6-linux-x86_64.zip
cd bowtie2-2.2.6
pwd
#~/software/bowtie2-2.2.6
echo 'export PATH=~/software/bowtie2-2.2.6:${PATH}' >> ~/.bashrc

---

• TopHat

wget https://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.0.Linux_x86_64.tar.gz
tar zxvf tophat-2.1.0.Linux_x86_64.tar.gz
cd tophat-2.1.0.Linux_x86_64
pwd
#~/software/tophat-2.1.0.Linux_x86_64
echo 'export PATH=~/software/tophat-2.1.0.Linux_x86_64:${PATH}' >> ~/.bashrc

---

• Cufflinks

wget http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.Linux_x86_64.tar.gz
tar zxvf cufflinks-2.2.1.Linux_x86_64.tar.gz
cd cufflinks-2.2.1.Linux_x86_64
pwd
#~/software/cufflinks-2.2.1.Linux_x86_64.tar.gz
echo 'export PATH=~/software/cufflinks-2.2.1.Linux_x86_64:${PATH}' >> ~/.bashrc

---

• samtools

wget https://github.com/samtools/samtools/releases/download/1.2/samtools-1.2.tar.bz2
tar jxvf samtools-1.2.tar.bz2
cd samtools-1.2
make
pwd
#~/software/samtools-1.2
echo 'export PATH=~/software/samtools-1.2:${PATH}' >> ~/.bashrc

---

• Bedtools

wget https://github.com/arq5x/bedtools2/releases/download/v2.25.0/bedtools-2.25.0.tar.gz
tar zxvf bedtools-2.25.0.tar.gz
cd bedtools2
make
cd bin
pwd
#~/software/bedtools2/bin
echo 'export PATH=~/software/bedtools2/bin:${PATH}' >> ~/.bashrc

---

• MACS14

###python_settings###
#Make_directory
mkdir -p ~/software/python_path/lib/python2.7/site-packages/

#.bashrc setting
echo 'export PYTHONHOME=/usr/local' >> ~/.bashrc
echo 'export PYTHONPATH=~/software/python_path/lib/python2.7/site-packages' >> ~/.bashrc
echo 'export PATH=~/software/python_path/bin:${PYTHONHOME}/bin:${PATH}' >> ~/.bashrc
echo 'export LD_LIBRARY_PATH=~/software/python_path/lib:${LD_LIBRARY_PATH}' >> ~/.bashrc

###MACS14_installation###
wget https://github.com/downloads/taoliu/MACS/MACS-1.4.2-1.tar.gz
tar zxvf MACS-1.4.2-1.tar.gz
cd MACS-1.4.2
python setup.py build
python setup.py install --prefix=~/software/python_path

---

• HTSeq(htseq-count)

###python_settings###
#Make_directory
mkdir -p ~/software/python_path/lib/python2.7/site-packages/

#.bashrc setting
echo 'export PYTHONHOME=/usr/local' >> ~/.bashrc
echo 'export PYTHONPATH=~/software/python_path/lib/python2.7/site-packages' >> ~/.bashrc
echo 'export PATH=~/software/python_path/bin:${PYTHONHOME}/bin:${PATH}' >> ~/.bashrc
echo 'export LD_LIBRARY_PATH=~/software/python_path/lib:${LD_LIBRARY_PATH}' >> ~/.bashrc

###HTSeq_installation###
wget https://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.6.1.tar.gz#md5=b7f4f38a9f4278b9b7f948d1efbc1f05
tar zxvf HTSeq-0.6.1.tar.gz
cd HTSeq-0.6.1
python setup.py build
python setup.py install --prefix=~/software/python_path

###PySam_installation###
pip install --install-option="--prefix=~/software/python_path" PySam

---

• SRA Toolkit

wget http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.5.5/sratoolkit.2.5.5-centos_linux64.tar.gz
tar zxvf sratoolkit.2.5.5-centos_linux64.tar.gz
cd sratoolkit.2.5.5-centos_linux64/bin
pwd
#~/software/sratoolkit.2.5.5-centos_linux64/bin
echo 'export PATH=~/software/sratoolkit.2.5.5-centos_linux64/bin:${PATH}' >> ~/.bashrc

---

• Trimmomatic

wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.35.zip
unzip Trimmomatic-0.35.zip
cd Trimmomatic-0.35

###Shell script preparation###
cat prep_file.sh
#!/bin/bash
java -jar "$0" "$@"
exit $?

###Make easy-to-use trimmomatic command###
cat prep_file.sh trimmomatic-0.35.jar > trimmomatic_core
chmod 755 trimmomatic_core
pwd
#~/software/Trimmomatic-0.35
echo 'export PATH=~/software/Trimmomatic-0.35:${PATH}' >> ~/.bashrc

---

• PARalyzer

wget https://ohlerlab.mdc-berlin.de/files/duke/PARalyzer/PARalyzer_v1_1_executable.tgz
tar zxvf PARalyzer_v1_1_executable.tgz
cd PARalyzer_v1_1
chmod 755 PARalyzer
pwd
#~/software/PARalyzer_v1_1
echo 'export PATH=~/software/PARalyzer_v1_1:${PATH}' >> ~/.bashrc

---

• cERMIT

wget https://ohlerlab.mdc-berlin.de/files/duke/transcription/cERMIT/Georgiev_2009_executable_with_sample_datasets_v1.01.tar.gz
mkdir cERMIT_v1_0
mv Georgiev_2009_executable_with_sample_datasets_v1.01.tar.gz cERMIT_v1_0
tar zxvf Georgiev_2009_executable_with_sample_datasets_v1.01.tar.gz
pwd
#~/software/cERMIT_v1_0
echo 'export PATH=~/software/cERMIT_v1_0:${PATH}' >> ~/.bashrc

---

• PhyloGibbs

wget https://www.imsc.res.in/~rsidd/phylogibbs/linux-static/phylogibbs
chmod 755 phylogibbs

---

• PhyloGibbs-MP

wget https://www.imsc.res.in/~rsidd/phylogibbs-mp/linux64/phylogibbs-mp-2.0-linux64.tar.gz
tar zxvf phylogibbs-mp-2.0-linux64.tar.gz
cd phylogibbs-mp-2.0-linux64/program
pwd
#~/software/phylogibbs-mp-2.0-linux64/program
echo 'export PATH=~/software/phylogibbs-mp-2.0-linux64/program:${PATH}' >> ~/.bashrc

---

• STAR

git clone https://github.com/alexdobin/STAR.git
cd STAR/bin/Linux_x86_64_static
pwd
#~/software/STAR/bin/Linux_x86_64_static
echo 'export PATH=~/software/STAR/bin/Linux_x86_64_static:${PATH}' >> ~/.bashrc

---

• RiboTaper

wget https://ohlerlab.mdc-berlin.de/files/RiboTaper/RiboTaper_v1.3.tar.gz
tar zxvf RiboTaper_v1.3.tar.gz
mv Version_1.3 RiboTaper_v1.3
cd RiboTaper_v1.3/scripts
pwd
#~/software/RiboTaper_v1.3/scripts
echo 'export PATH=~/software/RiboTaper_v1.3/scripts:${PATH}' >> ~/.bashrc

---

• RSEM

wget https://github.com/deweylab/RSEM/archive/v1.2.29.tar.gz
tar zxvf v1.2.29.tar.gz
cd RSEM-1.2.29/
mkdir bin
make
make ebseq
make install DESTDIR=/home/akimitsu/software/RSEM-1.2.29 prefix=/bin
cd bin
pwd
#~/software/RSEM-1.2.29/bin/bin
echo 'export PATH=~/software/RSEM-1.2.29/bin/bin:${PATH}' >> ~/.bashrc

---

• BWA

https://github.com/lh3/bwa/releases/download/v0.7.13/bwa-0.7.13.tar.bz2
tar jxvf bwa-0.7.13.tar.bz2
cd bwa-0.7.13/
make
pwd
#~/software/bwa-0.7.13
echo 'export PATH=~/software/bwa-0.7.13:${PATH}' >> ~/.bashrc

---

• Picard

#For java 1.7.x
#Download the latest version(picard-tools-1.119)
wget https://sourceforge.net/projects/picard/files/picard-tools/1.119/picard-tools-1.119.zip

---

• subread (featureCounts)

wget https://sourceforge.net/projects/subread/files/subread-1.5.0-p2/subread-1.5.0-p2-Linux-x86_64.tar.gz
tar zxvf subread-1.5.0-p2-Linux-x86_64.tar.gz
cd subread-1.5.0-p2-Linux-x86_64/bin
pwd
#~/software/subread-1.5.0-p2-Linux-x86_64/bin
echo 'export PATH=~/software/subread-1.5.0-p2-Linux-x86_64/bin:${PATH}' >> ~/.bashrc

---

• circos

wget http://circos.ca/distribution/circos-0.69-2.tgz
tar zxvf circos-0.69-2.tgz
pwd
#/home/akimitsu/software/circos-0.69-2/bin
echo 'export PATH=~/software/circos-0.69-2/bin:${PATH}' >> ~/.bashrc

---

• FUSIM

wget https://github.com/aebruno/fusim/raw/master/releases/fusim-0.2.2-bin.zip
unzip fusim-0.2.2-bin.zip

###Shell script preparation###
cat prep_file.sh
#!/bin/bash
java -jar "$0" "$@"
exit $?

###Make easy-to-use trimmomatic command###
cat prep_file.sh fusim.jar > fusim
chmod 755 fusim
mkdir bin
mv fusim bin
cd bin
pwd
#/home/akimitsu/software/fusim-0.2.2/bin
echo 'export PATH=/home/akimitsu/software/fusim-0.2.2/bin:${PATH}' >> ~/.bashrc