How to decide the bin size in interaction loops?

ay-lab / fithic

Fit-Hi-C is a tool for assigning statistical confidence estimates to chromosomal contact maps produced by genome-wide genome architecture assays such as Hi-C.

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How to decide the bin size in interaction loops? #40

Open shanwai1234 opened 3 years ago

shanwai1234 commented 3 years ago

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 commented 3 years ago

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 commented 3 years ago

Thank you for your answer!