13 months ago
University of Manchester, UK
If you use bedtools genomecov you can use a scaling factor.
bedtools genomecov -ibam input.bam -bg -scale X -g genome.chrom.sizes > normalised.bg
where X is the scaling factor. The scale could be for each sample 1,000,000/mapped reads, or each sample divided by the mean of mapped reads for each sample.
You can then use:
wigToBigWig -clip normalised.bg genome.chrom.sizes normalised.bw