sequencing depth for loops

[BenxiaHu]

Hello,
I want to call loops using FitHiC2 at 10kb resolution. Do you know how many valid paired reads are rquired by FitHiC2 to call loops at 10kb resolution? 300million valid paired reads?

[ay-lab]

300M is a bit on the lower end for 10kb but should be good enough. Assuming it is human or mouse.

[BenxiaHu]

yes, the Hi-C data is from human tissue.
based on your experience, do you think that how many valid paired reads should be fine? 500M or 1 billion?

[ay-lab]

500M should be sufficient for 10kb. 1B valid reads should allow you to do 5kb.

[BenxiaHu]

great. Thanks.
How do you calculate that? or just based on your experience?

[ay-lab]

based on experience and the past datasets we worked with

[BenxiaHu]

thanks.