User: LGMgeo

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LGMgeo30
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Location:
European Union
Last seen:
11 hours ago
Joined:
3 years ago
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v*****************@inserm.fr

Posts by LGMgeo

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Comment: C: TAD (Topologically Associating Domain) boundaries
... Could you then share their answer? Thanks ...
written 5 weeks ago by LGMgeo30
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Comment: A: TAD (Topologically Associating Domain) boundaries
... Dear Igor, as you seem to be a TAD specialist, I have a last question. We know that disruption of TAD boundaries with structural variation can affect the expression of nearby genes, and this can cause disease. Do you have any idea of if it can affect all the genes of the TAD? Or only those located ...
written 9 weeks ago by LGMgeo30
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Comment: C: TAD (Topologically Associating Domain) boundaries
... Really interesting and clear, many thanks! ...
written 9 weeks ago by LGMgeo30
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Comment: C: TAD (Topologically Associating Domain) boundaries
... Or you can do a grep command: grep "bed" listOfFiles.txt > TADbedFiles.list.txt There are also some bedpe files (new format to allow inter-chromosomal feature definitions). You can keep them or not. ...
written 9 weeks ago by LGMgeo30
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Comment: C: TAD (Topologically Associating Domain) boundaries
... By the way, do you have any idea of the TAD boundaries size? Is there a clear definition? ...
written 9 weeks ago by LGMgeo30
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Comment: C: TAD (Topologically Associating Domain) boundaries
... Yes I was. Click the "bed bed3+" button on your link (else the "file.txt" is blank). Then, click the “Download” button to download a “files.txt” file that contains a list of URLs to a file containing all the experimental metadata and links to download the file. Then, keep only the *.bed URLs in y ...
written 9 weeks ago by LGMgeo30
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Comment: C: TAD (Topologically Associating Domain) boundaries
... Thanks Igor for your link! It gives access to 55 human TAD BED files (not sorted, and with from 3000 to 6000 TAD per file): 31 files on hg19 24 files on hg38 ...
written 9 weeks ago by LGMgeo30
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Comment: C: TAD (Topologically Associating Domain) boundaries
... Ok, I'm certainly wrong but I'm not sure to understand. In the above paper, authors said that clusters of CNE (described previously as GRBs) strongly coincide with topological organisation, predicting the boundaries of hundreds of topologically associating domains (TADs) in human. So, according to ...
written 9 weeks ago by LGMgeo30
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Comment: C: TAD (Topologically Associating Domain) boundaries
... For human genome, the supplementary data 1 looks good. Many thanks. (supplementary data 2 is for *Drosophila*) If it may interest someone else, I extracted following informations from the supplementary data 1 - genome version: hg19 - 816 genomic regulatory blocks (GRBs), predicting the boundaries ...
written 9 weeks ago by LGMgeo30
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Comment: A: TAD (Topologically Associating Domain) boundaries
... Sorry, in human genome ...
written 9 weeks ago by LGMgeo30

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Student 5 weeks ago, asked a question with at least 3 up-votes. For TAD (Topologically Associating Domain) boundaries

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