How to run RE chromunity analysis?

[hzjsxu]

Hi @asd1289,

I have read your paper on pore-c—an excellent work.

Here, I wonder how you perform the whole genome RE chromunity analysis , i.e. the parameters and resolutions used in paper? I tried to carry out the RE chromunity in 50kb resolution, set subsample.frac to 0.1 ~ 0.8) and different shave parameters (set cthresh and bthresh to 5), but all experiments cannot run successfully. It seemed that R run out of memory (I run this in a node with 6TB memory). The problem occurred when using chromunity::annotate function.

Could you please guide me to run RE chromunity successfully?

[asd1289]

Hi @hzjsxu You can try one or more of the following:

1. Make sure the k is set to 3. Higher k's will explode the problem space.
2. If there are some very large chromunities, try excluding them before running synergy
3. Try smaller bin sizes such as 25kb/10kb

Hopefully this help solve the issue.

[hzjsxu]

OK, I will try this again. Thanks !