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HenrikBengtsson / TopDom

R package: TopDom - An efficient and Deterministic Method for identifying Topological Domains in Genomes
https://cran.r-project.org/package=TopDom
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Question about the Tags column #9

Open QianzhaoJ opened 5 years ago

QianzhaoJ commented 5 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. Which of these two, the edges of regions tagged ‘domian’ or these region taged ‘boundary’, represents ‘TAD boundairs’ ? 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

HenrikBengtsson commented 5 years ago

Hi @QianzhaoJ, all these are great questions.

However, please see Issue #11.

sidiropoulos commented 4 years ago

Hi, I have the same question as @QianzhaoJ. I tried to looked into the source code but I couldn't go very far. @HenrikBengtsson Should we refer to the authors of the paper with such questions? And if so, is it possible to have someone answer on this thread so the answer can be used as a reference for users with the same issue? Best, Nikos

HenrikBengtsson commented 4 years ago

Hi @sidiropoulos, yes, I suggest trying to go to the source to figure out whether this is by design or a mistake.

In lieu of an official TopDom forum, feel free to use this repos/issue tracker as an official forum and point of reference. If the authors could reply directly here that would be a benefit to the community, but if not, feel free to paraphrase any answers they give here.

If there's new information learned, I'm happy to include it in the help pages of the package too. I'm open to edits via PRs (pull requests) here on GitHub.

WiamMansouri commented 2 years ago

Hi , please i like to know if you had the explanation of the tag boundary, (Shouldn't there be only one boundary between two neighbouring TAD domain ?) And thank youuu