Normalize

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

• min-max: Find the genomic min and max values, then scale them between [0,1] or some-user defined range. The max value can be calculated as (1) the absolute max value across the genome (traditional definition of min-max) or (2) you can set a percentile cutoff to use as the max value. Option 2 improved robustness to outlying high ATAC-seq signal and maxATAC prediction accuracy. Specifically, we use the 99th-percentile max value instead of the absolute max value, and, given important performance ramifications, is the default.
• zscore: Set the mean value to 0 with a standard deviation of 1.
• arcsinh: Transform the values using an inverse hyperbolic sin transformation (arcsinh)

Example

maxatac normalize -i GM12878_RP20M.bw -name GM12878_minmax -o ./test --method min-max --max_percentile 99

Required Arguments

-i, --signal

The input bigWig file to be normalized.

-n, --name, --prefix

The name used to build the output filename. This can be any string.

Optional Arguments

--blacklist_bw

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 bigWig file.

-c, --chroms, --chromosomes

Define the chromosomes that are normalized. Only the chromosomes in this list will be written to the output file. The current default list of chromosomes are restricted to the human autosomal chromosomes:

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

Note: this argument MUST be specified in conjunction with --genome and --chrom_sizes if the input file was aligned to a genome build other than hg38.

--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

-cs, --chrom_sizes, --chromosome_sizes

Define the chromosome sizes file. The current default file are the chromosome sizes for hg38. Note: this argument MUST be specified in conjunction with --genome and --chromosomes if the input file was aligned to a genome build other than hg38.

--genome

The genome build that was used for alignment of the input file. Default: hg38.

--loglevel

Set the logging level. Currently, the only working logging level is ERROR.

--max

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

--max_percentile

If the specified 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.

--max_zooms

The number of zoom levels that should be computed for the normalized bigWig file. Zoom levels are pre-computed summary statistics that enable fast zooming into/out of a genomic region in a bigWig file when a visualization tool (e.g., IGV, UCSC Genome Browser). Lower values of this parameter result in slower loading of bigWig files in visualization tools, while higher values of this parameter result in a large memory overhead. The range of potential parameter values is (0-10). Default: 5. Note: if this argument is set to 0, the resulting bigWig files are NOT compatible with other bigWig tools (e.g., deepTools) and cannot be visualized using tools like IGV and the UCSC Genome Browser. Please see: https://github.com/deeptools/pyBigWig/blob/master/README.md for additional details.

--method

The method to use for normalization. Default: min-max

• min-max: Find the genomic min and max values, then scale them between [0,1] or some user-defined range. The max value can be calculated as (1) the absolute max value across the genome (traditional definition of min-max) or (2) you can set a percentile cutoff to use as the max value. Option 2 improved robustness to outlying high ATAC-seq signal and maxATAC prediction accuracy. Specifically, we use the 99th-percentile max value instead of the absolute max value, and, given important performance ramifications, is the default.
• zscore: Set the mean value to 0 with a standard deviation of 1.
• arcsinh: Transform the values using an inverse hyperbolic sin transformation (arcsinh)

--min

The minimum value for min-max normalization. Default: 0

-o, --output, --output_dir

Define the output directory. If the output directory is not supplied, a directory called ./normalize will be created in the current working directory.