Loop and TAD calling from HiC reads using HOMER

Question

[arsala521]

Hi,

I have HiC reads from an HiC experiment and I am using HOMER to call loops and TADs. The numbers I am getting are like:

Total TADs: 5024; Total Loops : 254

As multiple loops are expected in a TAD so numbers of loops should be higher than the number of TADs. That's why I am not sure how to justify the numbers I am getting.

I made sure I am not doing any mistake in the HOMER pipeline of loop/TAD calling and I followed all the steps in the tutorial here: http://homer.ucsd.edu/homer/interactions2/index.html Unfortunately I don't have any other loop calling program installed right now and HOMER is easy to install and run.

If someone working with HiC data analysis and TAD/loop calling from HiC reads can please comment on this? I also tried contacting HOMER at the given address here: [e-mail] but I didn't hear back. I also put HOMER in the post tag hoping if I can get connected with the relevant support.

Thanks