Model Overview

The ultimate use of this model is to denoise ATAC-seq data and create a higher-quality signal for a much cheaper cost compared to collecting high quality data.

Model Architecture

The model is a residual neural network consisting of 5 residual blocks that produce the denoised ATAC-seq signal, followed by 2 additional residual blocks and a sigmoid layer to produce classification (peak calling) output. All residual blocks are composed of 1-dimensional convolutional layers and ReLU activations.

Training

This model was trained on low cell count single-cell ATAC- seq data from human blood cells (CD4+, CD8+, and pre-B cells). Uses the dsci-ATAC protocol. Clean data read depth is 13 Million, noisy data read depth is 1 Million. Noisy cell count is 450, clean cell count is 6000. Data was obtained from Lareau, C. A. et al. Droplet-based combinatorial indexing for massive-scale single-cell chromatin accessibility. Nat. Biotechnol. 37, 916–924 (2019).

Dataset

Noisy Data: Click on the File Browser tab above. Click on train_data -> noisy_data.

Clean Data: Click on the File Browser tab above. Click on train_data -> clean_data.

Performance

No performance information available at this time.

How to Use this Model

Take a look at the notebook tutorial given in the AtacWorks repository: https://github.com/clara-parabricks/AtacWorks/blob/master/tutorials/tutorial1.ipynb

Change the links at Step 2: Download data in the tutorial to point to the files at this location.

Pretrained Models: The best performing model can be found under the File Browser tab, models directory.

Configs: AtacWorks has the ability to take in config files that specify various command line options. This makes it easy to share the exact parameters the model was trained with. You can find the configs under the File Browser tab, configs folder.

Input

The input data for this model consists of noisy ATAC-seq coverage tracks. The labels to train the model are clean ATAC-seq coverage tracks and peak calls based on the clean coverage tracks.

Output

This model learned to denoise a 450 cell count atac-seq data to resemble a 6000 cell count data. The output from atacworks is two bedGraph, optionally BigWig files. One containing denoised tracks and other containing denoised peaks.

Output Files: For the convenience of users, we have uploaded the output files generated by AtacWorks. They can be found under File Browser tab, output directory.

Limitations

No information about known limitations available at this time.

Reference

Lal, A., Chiang, Z.D., Yakovenko, N. et al. Deep learning-based enhancement of epigenomics data with AtacWorks. Nat Commun 12, 1507 (2021). https://doi.org/10.1038/s41467-021-21765-5

License

The model architecture, training and inference pipelines for this model were developed by the NVIDIA Genomics team. The relevant source code is open sourced under a custom NVIDIA license available here.