.. _atac:

scATAC-Seq Workflow
===================

The scATAC-Seq workflow starts with feature-by-barcode matrices and performs various 
QC steps and batch correction, clustering optimization, differential testing, and combines
everything together into a single Seurat object for easy exploratory visualization and 
downstream analysis.

Specifically, the workflow does the following:

    - Load different formats (HDF5, MEX, RDS) from cellranger pipelines
    - Downloads genome annotation files
    - Normalizes and/or scales data based on assay type
    - Reduces technical variation and batch effects
    - Linear dimensional reduction
    - (Optional) optimizes clustering parameters
    - Non-linear dimensional reduction for visualizations
    - Weighted Nearest Neighbor analysis
    - Differential testing of chromatin accessibility and overrepresented motifs

To configure a scATAC-Seq experiment, see :ref:`config-atac`.

.. image:: ../dags/atac/dag-5.png