How to decide the bin size in interaction loops?

[shanwai1234]

Hello,

I am running fithic. From the output, it only shows the midpoint of fragment in interaction loops. I am just wondering how I can come to determine the bin size to know which range of genomic regions can be potentially interacted with another range of genomic regions? I assume just the output from previous FitHiChip results. Thank you!

Zhikai

[ay-lab]

you should already be giving it a binsize/resolution parameter so you would know from the beginning.
If the midpoint is 25000 and you have used 10kb as your resolution then the bin spans 20000-30000

[shanwai1234]

Thank you for your answer!