This repository contains an ATAC-Seq pipeline using Snakemake.

Folders and files should be self-explanatory, however, a few notes:
  1) The doc folder contains various documentation. The "old" subfolder can be safely ignored. See the various PDF files for a (beta) version of the documentation and some other helpful information regarding how to run the pipeline, how to procvess ATAC-Seq data etc.
  2) The example folder is important. Use this to test if you run the pipeline using a small example analysis consisting of two samples.
  3) The src folder contains the source of the project.

The Git does NOT contain the data subdirectory in examples, so if you clone via Git, make sure to copy this folder manually: /g/scb2/zaugg/carnold/Projects/AtacSeq/example/data