CNV-correction pipeline adjustments

[lu-r-lu]

Hello

I have a couple of question around correct-cnv:

1. Is cooler balance the only option for the ICE-balancing prior to correction? Is it also possible to use HiCexplorer's hicCorrectMatrix correct?
2. Is cnv-correct compatible with WGS-derived CNV values? I have a processed Control-freec output (bedGraph-like) I would like to use and was curious if there are any downsides as opposed to using Hi-C derived CNV values.

Thanks you very much in advance
L.

[XiaoTaoWang]

1. Yes, cooler balance is currently the only supported option.
2. Yes, cnv-correct is compatible with CNV segments derived from Control-FREEC or other WGS-based tools , although this has not been extensively tested.

Xiaotao

[lu-r-lu]

Thank you, Xiaotao!

All the best,
L.