HTSeq is a Python package designed to take in sequence data from high-throughput genetic sequencing technologies and then process this data for further analysis. The package can handle reading and writing of sequence data, analysis of read quality, and much more. The full documentation can be found at the official website for the package.

Using HTSeq on RCC Resources

HTSeq must be installed in a virtual environment. The basic workflow for this is as follows:

$ python3 venv -m ~/test     # You can name the virtual environment anything you want
$ source ~/test/bin/activate # activates the virtual environment
$ pip install HTSeq         

Once you have the package, you should be able to run HTSeq from within your virtual environment by running:

$ python3
>> import HTSeq

To exit python, simply type the command exit(), and to exit the virtual environment, simply type the command deactivate.