Running the example dataset

We provide an example data set, based on samples form Genome in a Bottle samples, that can be used to test the setup.

Please note that the Genome in a Bottle samples are not pluripotent stem cells, so interpretation of the data is not really possible.

Obtain the example data

The example input data can be downloaded from zenodo, or directly on the command line:

wget https://zenodo.org/records/16962381/files/example_input_data.zip
unzip example_input_data.zip

If you download the data through the web-browser make sure to unzip it also. Even when using WSL, it is recommended to leave all StemCNV-check files on the linux file system to improve performance.

Run the example data

Note

Working with the example data requires, that you have installed StemCNV-check.

The example data fileset contains all necessary input files as well as a fully filled in sample table and config file, so you can proceed to generation of static data and data analysis right away:

  • Make sure you have an open terminal, located in unpacked the example data folder containing the config.yaml and sample table files. If you used the above commands to download the files from the command line this should already be the case.

  • Start the preparation of the static data for the example data

    stemcnv-check make-staticdata

    Note

    If you have not used StemCNV-check before, this step will include the download of reference fasta and gtf files for the human genome. This download will require some disk space and a bit of time.

    If you are an experienced user, you can also provide paths to the necessary fasta and gtf files from your own system. This requires entries in the global_settings section of the config.yaml file, which is included with medium detail when creating example files.

    Tip

    If StemCNV-check encounters issues automatically download files, please see the Troubleshooting section for potential solutions to common issues.

  • Finally start the StemCNV-check workflow for the example data:

    stemcnv-check run

After performing all these steps you should have complete output for all 6 samples in the data folder.

You can also download the example output data, created with StemCNV-check version 1.0, to compare them with your newly generated files.