Transcription Factor Binding Prediction from ATAC-seq and scATAC-seq with Deep Neural Networks

View the Project on GitHub MiraldiLab/maxATAC


The peaks will take a maxATAC prediction .bw signal track and call intervals of TFBS that meet a given confidence threshold. These TFBS intervals will be output as BED intervals that can be visualized and used for downstream analysis.

The peaks function takes as input a bigwig signal track and will output bins that are above a given threshold.


maxatac peaks -i -o ./peaks -bin 32 -cutoff_file ARID3A_validationPerformance_vs_thresholdCalibration.tsv

Required Arguments

"-i", "--input_bigwig"

The input maxATAC bigwig file.

"-cutoff_file", "--cutoff_file"

The cutoff file provided in /data/models that corresponds to the average validation performance metrics for the TF model.

Optional Arguments

Note on abbreviations:

"-cutoff_type", "--cutoff_type"

The cutoff type (i.e. Precision, Recall, F1, log2FC). Default: F1.

"-cutoff_value", "--cutoff_value"

The cutoff value for the cutoff type provided. Note precision, recall, and F1-scores range 0-1, while better-than-random log2FC scores range from 0 to infinity. Example: .7

"-prefix", "--prefix"

The prefix to use for the output file name.

"-bin", "--bin_size"

The bin size (TFBS interval length) used for calling peaks. Default: 32 bp, based on the benchmarking intervals predictions. 32 bp, the resolution of the maxATAC models, is also a good option.

"-o", "--output"

The path to the output directory to write the bed.


The chromosomes to limit peak calling to. Default: Autosomal chromosomes that are used in training and evaluation.