CAIC normalisation very slow for high resolution

[csijcs]

Do you have any recommendations for speeding up the CAIC normalisation for high resolution matrices?

I have called the CNVs and am supplying the seg.bed file along with the abs.bed and .matrix files to the ice_cnv.py script.

It works great and quite fast for 1Mb and 500Kb, but when I get down to 100Kb it is almost prohibitively slow. I would like to run the normalisation at 40Kb, but it would be impossible at the current speed.

The LOIC runs pretty fast, the rate limiting step is in estimating the CNV bias.

[nservant]

Hi,
Unfortunately, I do not have a magic answer. I know that it can take times and memory consuming for high resolution data ...
The only thing I could advice would be to try to run it per chromosome at high res, instead of genome-wide.
In addition, if we are talking about large CNVs, I think that the effect at 40kb (typically at TADs level) would be limited (except at the CNV breakpoints I guess).
We never really investigated the CNV effect at the TADs levels actually, but rather focus on the compartments calling (around 250kb resolution)
Sorry for that. Best