Polyase tutorial

Allelic gene and isoform expression analysis in potato

The jupyter notebook tutorial demonstrates how to use the polyase package to analyze allele-specific expression (ASE) in tetraploid potato using long-read RNA-seq data. The tutorial covers loading the data, calculating allelic ratios, filtering, statistical analysis, and visualization of ASE patterns. The notebook is available here. Files necessary for this tutorial are deposited on Zenodo here.

Running the tutorial locally

Create a conda environment that also includes ipykernel to run jupyter notebooks:

conda create -n polyase python=3.12 ipykernel pip && conda activate polyase && pip install polyase && pip install pyranges

If you get an error regarding the installation of pyranges (a known issue on mac and windows), then try to install it via conda:

conda install -c bioconda pyranges

Running the tutorial within Docker

A Docker image with PolyASE and JupyterLab is available on Docker Hub.

  1. Download the tutorial notebook and input data:

  2. Unzip the input data and place the notebook and all data files into a local notebooks/ folder.

  3. Start the container, mounting your notebooks/ folder:

    docker run --rm -p 8888:8888 \
  -v $(pwd)/notebooks:/home/user/notebooks \
  nadjano/polyase:1.3.3

  4. Open http://localhost:8888 in your browser, open potato_polyase.ipynb, and update any file paths in the notebook to /home/user/notebooks/.

potato_polyase