This tutorial assumes that

  1. You know how to use BEDTools (if not, check out the BEDTools documentation)

  2. You know how to use Python (if not, check out some tutorials like Learn Python the Hard Way)

A brief note on conventions

Throughout this documentation I’ve tried to use consistent typography, as follows:

  • Python variables and arguments, as well as filenames look like this: s=True

  • Methods, which are often linked to documentation look like this: BedTool.merge().

  • Arguments that are passed to BEDTools programs, as if you were on the command line, look like this: -d.

  • The “>>>” in the examples below indicates a Python interpreter prompt and means to type the code into an interactive Python interpreter like IPython or in a script. (don’t type the >>>)