Processing ATAC-Seq Data

About

proatac is an open-source command-line toolkit that performs robust and scalable preprocessing of ATAC-Seq data. Specifically, we’ve implemented our workflow using Snakemake, a robust, scalable computational workflow platform. Various snakefiles are wrapped alongside meta-data annotations and various object-oriented constructs and distributed as a Python 3 package. The figure below provides a brief overview of the functionality of the proatac pipeline.

Installation

• Install stable version through PyPi
• Install via GitHub
• Installing proatac as an environment module.

Dependencies

• Getting proatac running

Trimming

• Optimized adaptor trimming
  • Bulk and C1-based single cell trimming.
  • Droplet-based barcode quantification and annotation

Alignment

• Optimized adaptor trimming
  • Bulk and C1-based single cell trimming.
  • Droplet-based barcode quantification and annotation

Annotating peaks

• Built-in annotation
  • Mitochondrial Blacklist
  • TSS Annotation
  • Bedtools Genomes
  • Missing a reference genome?

FAQ

• Single end reads?
• I found a bug / error; what do I do?
• I ran proatac; now what do I do?

Author

The primary developer is Caleb Lareau in the Buenrostro Lab.

Citation

If you use proatac in your research, please cite our tool at the following URL:

http://buenrostrolab.com/proatac

Bugs / Errors

Please let us know if you find any errors/inconsistencies in the documentation or code by filing a new GitHub Issue.