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

View the Project on GitHub MiraldiLab/maxATAC


The average function will average multiple bigwig files into a single bigwig file.


maxatac average --bigwigs *.bw --prefix IMR-90 --output ./test --chroms chr1

Required Arguments

-i, --bigwigs

This argument is reserved for the input bigwig files to be averaged together. You could use a *.bw wildcard to make a list of bigwig files as input or provide the path to two bigwig files.


This argument is reserved for the prefix used to build the output filename. This can be any string. The extension .bw will be added to the filename prefix.

Optional Arguments


This argument is used to define the chromosome sizes file that is used to calculate the chromosome ends. The current default is for hg38.


This argument is used to define the chromosomes that are averaged together. Only the chromosomes in this list will be written to the output file. The current default list of chromosomes are restricted to the autosomal chromosomes:

chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22


This argument is used to define the output directory. If the output directory is not supplied a directory called ./average will be created in the current working directory.


This argument is used to set the logging level. Currently, the only working logging level is ERROR.