STEP2: Install Software

Download and configure your software

Fastqc

URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/

# Move into Software folder
cd RNASeq_Gene_Expression_Analysis/Software

# Download the Fastqc to this folder using wget
wget https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.7.zip

# Decompress the folder
unzip  fastqc_v0.11.7.zip

# Change the directory to Fastqc
cd FastQC

# Change the executable permission of fastqc file
chmod a+x ./fastqc

# Check the software

./fastqc -h

BBduk

URL: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbduk-guide/

# Move into Software folder, assuming you are inside FastQC folder
cd ../

# Download the BBduk to this folder using wget
wget https://sourceforge.net/projects/bbmap/files/BBMap_38.23.tar.gz

# Extract files
tar -xvzf BBMap_38.23.tar.gz

# Change the directory to bbmap
cd bbmap

# Check the software
./bbduk.sh

HISAT2

URL: https://ccb.jhu.edu/software/hisat2/index.shtml

# Move into Software folder, assuming you are inside bbmap folder
cd ../

# Download the HISAT2 to this folder using git clone
git clone https://github.com/infphilo/hisat2.git

# Change the directory to hisat2
cd hisat2

# Create binaries
make

# Check the software
./hisat2

STAR

URL: https://github.com/alexdobin/STAR

# Move into Software folder, assuming you are inside hista2 folder
cd ../

# Download the STAR to this folder using git clone
git clone https://github.com/alexdobin/STAR.git


# Check the software
./STAR/bin/Linux_x86_64/STAR

featureCounts

URL: http://subread.sourceforge.net

# Download the Subread to this folder using wget, but save it as subread-1.6.2.tar.gz
wget https://sourceforge.net/projects/subread/files/subread-1.6.2/subread-1.6.2-Linux-x86_64.tar.gz -O subread-1.6.2.tar.gz

# Extract files
tar -xvf subread-1.6.2.tar.gz 

# Check the software
./subread-1.6.2-Linux-x86_64/bin/featureCounts

Alternative way of loading Software on OSC

# Check software available in the OSC
module avail

# Select subread/1.5.0-p2 from the list
module load subread/1.5.0-p2

# Check loaded software
module  list

# You can unload the module for now
module unload subread/1.5.0-p2

Q1:

Install multiQC by yourself

Cleaning archived files

go_wd
cd RNASeq_Gene_Expression_Analysis/Software/
rm BBMap_38.23.tar.gz fastqc_v0.11.7.zip subread-1.6.2.tar.gz

DESeq

URL: https://bioconductor.org/packages/release/bioc/html/DESeq2.html

# Load R from the module list
 module load R/3.5.0

# Get access to R shell
R

# Enter following and hit enter
> source("https://bioconductor.org/biocLite.R")
# Then, 
> biocLite("DESeq2")