conservation analysis when only a few syntenic blocks are available

[zy041225]

Hi,

I would like to compare the Hi-C maps but only a few (e.g. less than five, or even one) syntenic blocks (≥ 1Mb) are available. In my understanding, the raw SN and SSIM calculation do not depend on the sample size, but the z-SSIM will be affected by the sample size. I'm wondering, in my case, if the sample size is small, is it reasonable to use chess to quantify the contact map differences?

Many thanks

Best,
Yang

[liz-is]

Hello,
I don't personally have experience using CHESS to compare between species, but it sounds like this is an ideal use case for the --background-query option, which will run comparisons between all regions of the genomes (non-syntenic), which can then be used to calculate a p-value for the similarity of your syntenic regions. @nickmachnik knows more about this, maybe he can give some more specific guidance (I'm realising now that the docs are not very detailed for this part!)

[nickmachnik]

I agree with @liz-is, if you need to put your comparison results into context of some random expectation, using the --background-query flag is an option. Your reference block will then be compared to the whole query genome, in a block size equal to the syntenic query block. Whether that is a meaningful background model depends on the goal of your analysis.

[zy041225]

I see. Thank you.