H5 & cool file - spike in normalization

[CMylonas]

Hello,

I suggested a few months ago an implementation for HicNormalize for spike-in controls. I see that it has been added as a future request so thank you for that.
In the interim, is there another quick way (either a bash script or any changes I can make to hicNormalize.py) to multiply either .h5 or .cool files by a specific value calculated from my spike-in controls?

Thanks for the great software

Best,

Constantine

[joachimwolff]

Hi,

I implemented it, see branch spike_in.

Usage example:

hicNormalize --matrices gm12878_10kb_chr1.cool imr90_10kb_chr1.cool --normalize multiplicative --multiplicativeValue 2 -o gm12878_double.cool imr90_double.cool

Let me know if you need help to install HiCExplorer from a branch.

Best,

Joachim