Configure your PEP project files

To run your own samples, you'll need to organize them in PEP format, which is explained in how to create a PEP and is universal to all pipelines that read PEPs, including PEPATAC. To get you started, there are multiple examples you can adapt in the examples/ folder (e.g. example test PEP). In short, you need two files for your project:

  1. project config file -- describes output locations, pointers to data, etc.
  2. sample table file -- comma-separated value (CSV) list of your samples.

The sample table file must specify these columns:

  • sample_name
  • library ('ATAC' or 'ATACSEQ' or 'ATAC-seq')
  • organism (e.g. 'human', 'mouse', or 'drosophila' et cetera)
  • read1
  • read2
  • whatever else you want