snATAC-seq

Repository to try and test snATAC-seq analysis.

Initialize and match git repository:

git init
git remote add origin https://github.com/giuditta2024/snATAC-seq.git
git branch -m master main   # rename master to main 

Remember to add the folder data/ to the .gitignore file.

Then, download the required data:

sh download_data.sh

# move them in the data folder
mv atac*.* data/

Analysis in R

Refer to the Rmd.

Warning: To be updated

Analysis in Python

I will follow a couple of tutorials:

• Single Cell best practices
• EpiScanpy documentation

Regarding python conda enviroment:

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

conda create --name scATAC-env anndata matplotlib numpy pandas scanpy scipy scikit-learn seaborn
conda activate scATAC-env
conda install -c bioconda pyliftover bamnostic pysam

Now we want to add the conda enviroment to the jupyter notebook:

conda install ipykernel
python -m ipykernel install --user --name=scATAC-env --display-name "Python (scATAC-env)"