Genome data analysis in Python

Genome data analysis in Python

Activity by Hannes Svardal, 24 January 2018

 

A brief tutorial on the use of jupyter notebooks and the python data analysis library pandas for genomic data analysis.

Jupyter notebooks can run locally or on a server. You access them in your browser.

To start the jupyter server

• Log into your amazon cloud instance: ssh [email protected] (replace my-ip-here with your instance’s address)
• Navigate into the tutorial directory: cd ~/workshop_materials/03a_genome_data_analysis_python/
• Start the notebook server: jupyter notebook --no-browser --port=7000 --ip=0.0.0.0
• In your local browser, navigate to the web address: http://my-ip-here.compute-1.amazonaws.com:7000
• On the web page, type in the password evomics2018

Now the tutorial continues within the jupyter notebook that you opened in you browser (named “201801_jupyter_pandas_tutorial.ipynb”; you can download the notebook for later reference here). Click on the notebook to open it, then skip the first few lines, and begin the tutorial on the line saying “Now you should have this notebook in front of you.”