Tuning the parameters (perc-zero, perc-undetected, pearson) for a relatively small dataset

[ZianFang]

Dear Chromosight developers:
First I'd like to thank you guys for developing such an excellent tool to call loop, and it is undoubtedly one of the best and popular loop callers among the users！
It is really necessary to call valid and precise loop to perform downstream analysis, so I am trying to apply chromosight to my Micro-C datasets, which is about 150M contacts for the mouse genome. I know it's a bit of an awkward size because it is a bit smaller than the lowest recommended size, but I still want to have a try. I have read about the closed issues and get to know that I may need to adjust the parameters (perc-zero, perc-undetected, pearson). But what can I do to assess the quality of loops called under different parameters? (I can only come up with this --- visualize the map and see with my eyes ). Can you give me some instructions on fine-tuning and assessing the parameters and the outcome? Or could you please share some professional experience?
Best wishes!
Woody

[axelcournac]

Dear Woody,
Thanks for your feedbacks. One thing you can do is to check if the loops you detect correspond to groups already established, for example you could compute the proportion of your detected loops that overlap cohesin peaks. I don't know if your cells are synchronized but in interphase, you should see an enrichment of your detected loops in cohesin or CTCF binding sites.

[ZianFang]

Dear axelcournac,
Thank you for your quick and detailed response! Fortunately, my bulk data are synchronized in G1 so I definitely will try the methods you provided :)
Could you please give some further instructions on which parameters (perc-zero, perc-undetected, pearson...) should be changed but not ruin the precision?(As I have mentioned I have low sequencing depth...)
My initial attempt implies that increasing perc-zero can more significantly increase the loop detected(from 300 to 600 for chr1), and a lower pearson is also the case. And different resolutions(5k,10k,20k) with the same default parameters can call loops of different scale(5k calls more diagonal loops than 10k and 20k).
And I have an even smaller Micro-C dataset of 10M contacts. Do you think I can apply chromosight to de novo call loop on it? I see previous answers that suggest ML-enhanced signal as input, but enhanced signals are just not that real, right?
In a word, thank you so much for you kindness and patience!
Best wishes!
Woody