normalize_bigwig.py¶

Normalize a BigWig signal to a fixed wigsum (equivalent to a target total read coverage). Outputs a wiggle file.

Usage¶

normalize_bigwig.py -i input.bw -o output.wig

Option	Description	Default
`-i`, `--bwfile`	Input BigWig file	Required
`-o`, `--output`	Output wiggle file	Required
`-t`, `--wigsum`	Target wigsum for normalization	100000000
`-r`, `--refgene`	Reference gene model in BED format (restricts normalization to gene regions)	Optional
`-c`, `--chunk`	Chromosome chunk size (bp) for processing	500000
`-f`, `--format`	Output format: `wig` or `bgr` (bedGraph)	bgr

Normalized signal in wiggle or bedGraph format.