maxATAC

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

View the Project on GitHub MiraldiLab/maxATAC

Normalize

The normalize function will normalize an input bigwig file based on the following approaches:

Example

maxatac normalize --signal GM12878_RP20M.bw --prefix GM12878 --output ./test --method min-max --max_percentile 99

Required Arguments

--signal

The input bigwig file to be normalized.

Optional Arguments

--method

This argument is used to determine which method to use for normalization. Default: min-max

--max_percentile

If method is min-max this argument will set the percentile value to use as the reported max value. The default is 99, so that default will be consistent with the ATAC-seq processing for the maxATAC models, where the 99th percentile value was used as the max value.

--min

The value to use as the minimum value for min-max normalization. Default: 0

--max

The value to use as the maximum value for min-max normalization. Default: False, so that max is calculated based on the ATAC signal track.

--clip

This flag determines whether to clip the values that are above the max value used in min-max normalization or to leave them as their real value. Default: False

--prefix

This argument is reserved for the prefix used to build the output filename. This can be any string.

--chroms

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

--chrom_sizes

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

--blacklist

The path to the blacklist bigwig file. This file is used to remove all the regions that are considered to have high technical noise. Default: maxATAC publication-defined blacklist.

--output

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

--loglevel

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