This is a workflow to analyze the human RNA sequencing data. There are several platforms available for RNA sequencing. However, new software and workflows develop and introduce every day. Here we introduce a workfow for analyzing the human RNA sequencing data Using GEMprep and Nextflow. By running this workflow, you will learn how to find out the RNAseq data from NCBI database and make GEM. Then, you will analyze the RNA sequencing data from homo sapiens.
- Make a GEM
- RNAseq Analysis
curl -s https://get.nextflow.io/ | bash
cp nextflow ~/bin
sudo apt update # Updates software repositories.
sudo apt install default-jre # Install Java
wget -qO- https://get.nextflow.io/ | bash # Compile nextflow
sudo cp nextflow /usr/local/bin # Adds nextflow to your PATH
nextflow # Type this to see if nextflow software installed
### Update the Linux software repositories
sudo apt-get update
### Download source code
export VERSION=3.10.0 && # adjust this as necessary
wget https://github.com/sylabs/singularity/releases/download/v$%7BVERSION%7D/singularity-ce-$%7BVERSION%7D.tar.gz && \
tar -xzf singularity-ce-${VERSION}.tar.gz && cd singularity-ce-${VERSION}
### Compile source code
./mconfig && make -C ./builddir && sudo make -C ./builddir install
### Install dependencies
sudo apt install -y \
build-essential \
libseccomp-dev \
pkg-config \
squashfs-tools \
cryptsetup \
libglib2.0-dev
cryptsetup
Singularity # Type this to see if singularity installed
wget https://go.dev/dl/go1.20.3.linux-amd64.tar.gz
sudo tar -C /usr/local -xzf go1.20.3.linux-amd64.tar.gz
echo $PATH | grep "/usr/local/go/bin"
source ~/.bashrc
nextflow run systemsgenetics/gemmaker -profile test,singularity
conda create -n gemprep python=3.6 matplotlib mpi4py numpy pandas r scikit-learn seaborn
source activate gemprep
git clone https://github.com/SystemsGenetics/GEMprep
cd GEMprep