Average

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

Example

Example command using only required flags:

maxatac average -i *.bw -n IMR-90

Example command using all flags:

maxatac average -i *.bw -n IMR-90 -o ./test -c chr1 -cs hg38.chrom.sizes

Required Arguments

-i

The input bigwig files. You could use a *.bw wildcard to make a list of bigwig files as input or provide the path to each file.

-n, --name, --prefix

The name string used to build the output filename. The extension .bw will be added to the filename.

Optional Arguments

-c, --chroms, --chromosomes

The chromosomes that are averaged together and written to output. 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.

-cs, --chrom_sizes, --chromosome_sizes

The chromosome sizes file for the reference genome used during alignment. The current default is set 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.

--max_zooms

The number of zoom levels that should be computed for the averaged 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.

--loglevel

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

-o, --output, --output_dir

The output directory. If the output directory is not supplied, the file will be created in the current working directory.