How to calculate all possible chromatin interactions in a given sample?

Question

[bioinfo89]

Hi All,

I am currently working on ChIAPET data of different cancer cell lines for a specific protein of interest. For the same, I am required to perform some statistical analysis which requires me to calculate all the possible chromatin interactions in each cell lines and then get a significance p-value. The observed number of chromatin interactions I have.

I am not sure how to calculate the above-mentioned total possible number of chromatin interactions in a sample. Can anyone help me with this part?

Thank you!

Answer 1

[kashiff007]

Use this tool for your analysis:

ChIAPoP: a new tool for ChIA-PET data analysis