normalized bigwigs

[MariaRosariaNucera]

Hi,
thank you for the useful tool! I just have one question on this part:
3.pseudo-code for generation of bigwig files from a bed file
libSize=cat sample1.bed|wc -l
scale=15000000/($libSize$SF)
genomeCoverageBed -bg -scale $scale -i sample1.bed -g mm9.chromSizes > sample1.bedGraph
bedGraphToBigWig sample1.bedGraph mm9.chromSizes sample1.bw*

I am not sure about the origin of this parameter 15000000. I would appreciate if you could explain why it was chosen.

Thank you!

[wge11]

The same question here: How can the scaling factor ($SF) be properly used when generating bigwig files?

Thanks!

[mdidish]

I think that the number 15000000 sets a target for normalization, ensuring all samples are scaled to an equivalent of 15 million fragments for better comparison.
It would be great if the authors could confirm.