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Questions about TAD calling #27
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Hi, thank you for your question.
TADtool uses the same algorithm to call insulating boundaries, and then has an additional step where it determines if any region between two boundaries has sufficient signal enrichment above background to be a TAD. TAD calling is very sensitive to parameter choices (insulation score window size, boundary strength cutoff, matrix resolution, etc), and also depends on the types of TADs you are interested in (large domains, nested domains). Therefore we have written TADtool, which allows you to find robust parameter ranges visually. However, our work has recently focused more on TAD boundaries, or the insulation score around genomic elements of interest, than TADs themselves. When you want to work with TADs directly, I would advise you to use multiple of the many available TAD callers, preferably with different algorithms, and get a robust consensus set of domains. Otherwise, depending on your question, it may be preferable to work with the insulation score directly, rather than the domains. I hope this is helpful! |
Thank you for your prompt reply.
Then, once one knows the boundaries, would not be TADs what is in-between? I believe that for my aim, to check if there is a difference in TAD borders among different conditions, the insulating boundaries are even better. Thank you again! |
Consider these examples:
In the first one, the TADs are indeed all regions between boundaries. That would also mean that every single base in a genome is part of a TAD. However, there are often large genomic regions with weak or no discernible structure between boundaries. I suppose it is a matter of definition if you want to call them TADs or not, but this is why TADtool requires a minimum level of signal between boundaries before a TAD is called. |
I agree with this concept if one considers the in-between in the second example as unique-extended boundaries
However, my perception is closer to this as well Thank you again for your time and clarification! |
Hi,
First, I would like to thank you for developing FANC tools and make it available.
It is helpful and it made simpler to analyse Hi-C data.
However, I'm once again asking for your help.
I intend to perform TAD calling and I would like to know what is the difference between
fanc boundaries
andtadtool
.It was not clear for me in this statement if
fanc boundaries
is a 1-TAD caller algorithm itself or 2-callstadtool
In case it is option 1- a TAD caller algorithm itself, which one has performed better on your hands?
Thank you for your time
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