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dekkerlab / crane-nature-2015

code associated with crane-nature-2015, 10.1038/nature14450
Apache License 2.0
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how to use insulation score to identify TAD domains #3

Open skytguuu opened 6 years ago

skytguuu commented 6 years ago

Hi,

Recently, I am interested to your developed method "insulation score". And I tried to use matrix2insulation.pl to identify TAD domains. I am curious about the result of this perl script. Because, the final result from matrix2insulation.pl is a summary about the boundary location. So, if I want to call TAD domains, is that simply divide the genome into several parts according to this boundaries? For example, if the boundary is chr1:4000000-4500000. Then the TAD domains are two parts？(chr1:0-4000000,chr1:4500000-...)

Could you give me some advise?

Thank you so much!

Best, Garen

min1992 commented 6 years ago

Hi, I am having the same question, so do you solve this question? thank you.

Best

skytguuu commented 6 years ago

Hi,

My problem has been solved. The reason is happened the label of my input matrix. I changed my middle lane of label as my reference genome.

blajoie commented 6 years ago

Sorry for the delay - for the original question, yes it is as simple as that. Simply divide the genome into segments defined by the boundary locations.

One caveat - you may wish to also consider the strength of the boundaries. e.g.

boundaries: chr1:2500000: strong chr1:5000000: weak chr1:5500000: strong

The above reflects 2 distinct tads, however, one may also wish to capture the fact that the major tad (chr1:2500000-5500000) also contains within it a smaller 'sub/nested' tad as evidenced by the much weaker boundary strength.

Hope that is clear.