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jasminezhoulab / TopDom

TopDom is a software tool to ideintify Topological Domains, which are basic builiding blocks of genome structrue. TopDom is computationally very efficient. Using detecting optimal polygon algorithm, TopDom detect topological domains in a linear time. As well as, this tool requires only a single parameter, which enable user to use easily.
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Output file question #3

Open QianzhaoJ opened 4 years ago

QianzhaoJ commented 4 years ago

Hi : I'm very interested in TopDom , and I have got some results using my 40kb-res data. However, I have some questions about the output. I’m very confused about the meaning of the tag column in .domain and .bed file . First, in output file, I found that there are many continuous regions and their tags are ‘domain’ , do these mean ‘TAD domain’ ? Second, I think ‘TAD boundaries’ means the edge of TAD domain. But ,The number of region whose tags are ‘boundary’ is few. so which of these two, the edges of regions tagged ‘domian’ or these region taged ‘boundary’, represents ‘TAD boundairs’ ? May be some TADs are consecutive , some not? The last question is that there are continuous regions tagged ‘boundary’ , such as : chr1 31920000 32040000 boundary chr1 32040000 32240000 boundary Shouldn't there be only one boundary between two neighbouring TAD domain ? Thanks for your time! Best wishes! Qianzhao

sidwekhande commented 8 months ago

Hi, I was wondering if there is an answer to this question - any guidance would be appreciated. Thanks!