{"action":"created","issue":{"url":"https://api.github.com/repos/deeptools/HiCExplorer/issues/211","repository_url":"https://api.github.com/repos/deeptools/HiCExplorer","labels_url":"https://api.github.com/repos/deeptools/HiCExplorer/issues/211/labels{/name}","comments_url":"https://api.github.com/repos/deeptools/HiCExplorer/issues/211/comments","events_url":"https://api.github.com/repos/deeptools/HiCExplorer/issues/211/events","html_url":"https://github.com/deeptools/HiCExplorer/issues/211","id":300566174,"number":211,"title":"TAD-sep score between 3 different replicates","user":{"login":"apaytuvi","id":11228225,"avatar_url":"https://avatars3.githubusercontent.com/u/11228225?v=4","gravatar_id":"","url":"https://api.github.com/users/apaytuvi","html_url":"https://github.com/apaytuvi","followers_url":"https://api.github.com/users/apaytuvi/followers","following_url":"https://api.github.com/users/apaytuvi/following{/other_user}","gists_url":"https://api.github.com/users/apaytuvi/gists{/gist_id}","starred_url":"https://api.github.com/users/apaytuvi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/apaytuvi/subscriptions","organizations_url":"https://api.github.com/users/apaytuvi/orgs","repos_url":"https://api.github.com/users/apaytuvi/repos","events_url":"https://api.github.com/users/apaytuvi/events{/privacy}","received_events_url":"https://api.github.com/users/apaytuvi/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2018-02-27T10:09:27Z","updated_at":"2018-04-18T07:57:20Z","closed_at":null,"author_association":"NONE","body":"Hi,\r\n\r\nI have 3 lines with different levels of compactness: high, medium and low. After ICE correction, I normalized the matrices so the sum of all counts is 100.000.000. Afterwards, I have calculated the TAD-separation scores using your software, by disabling the calculation of the z-scores by setting `use_zscores=False` in the code.\r\n\r\nLow compacted:\r\n![image](https://user-images.githubusercontent.com/11228225/36684018-722d425e-1b1f-11e8-8944-94526806563f.png)\r\nMedium compacted:\r\n![image](https://user-images.githubusercontent.com/11228225/36684082-a0dacd74-1b1f-11e8-931c-fa33b51e66f9.png)\r\nHigh compacted:\r\n![image](https://user-images.githubusercontent.com/11228225/36684054-8e6691c8-1b1f-11e8-91f4-1dab58eb092c.png)\r\nI plotted the TAD-sep scores for these 3 lines (1. high; 2. low; 3. medium):\r\n![image](https://user-images.githubusercontent.com/11228225/36684177-d29cba48-1b1f-11e8-9fec-d2c79fc726b1.png)\r\n\r\nI expected the low-compacted genome to have higher \"standard deviation\" than the medium-compacted, and the medium-compacted higher \"standard deviation\" than the high-compacted.\r\n\r\nHowever, the medium-compacted seems to have less TAD-sep score than the high-compacted... Does it make sense to you? Or am I doing something wrong?\r\n\r\nThanks."},"comment":{"url":"https://api.github.com/repos/deeptools/HiCExplorer/issues/comments/382298979","html_url":"https://github.com/deeptools/HiCExplorer/issues/211#issuecomment-382298979","issue_url":"https://api.github.com/repos/deeptools/HiCExplorer/issues/211","id":382298979,"user":{"login":"fidelram","id":4964309,"avatar_url":"https://avatars3.githubusercontent.com/u/4964309?v=4","gravatar_id":"","url":"https://api.github.com/users/fidelram","html_url":"https://github.com/fidelram","followers_url":"https://api.github.com/users/fidelram/followers","following_url":"https://api.github.com/users/fidelram/following{/other_user}","gists_url":"https://api.github.com/users/fidelram/gists{/gist_id}","starred_url":"https://api.github.com/users/fidelram/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/fidelram/subscriptions","organizations_url":"https://api.github.com/users/fidelram/orgs","repos_url":"https://api.github.com/users/fidelram/repos","events_url":"https://api.github.com/users/fidelram/events{/privacy}","received_events_url":"https://api.github.com/users/fidelram/received_events","type":"User","site_admin":false},"created_at":"2018-04-18T07:57:20Z","updated_at":"2018-04-18T07:57:20Z","author_association":"CONTRIBUTOR","body":"I think that your results make sense but I don't know if I understand correctly. What you call low compactness seems to me like a normal cell Hi-C in interphase with clear TADs. The high compactness looks like a cell in mitosis.\r\n\r\nIf the tracks that you present are in the same order as the figures on top, I would say that for the interphase case you should expect higher variation which is what I see. Otherwise for the mitotic case I see less variation.\r\n\r\nDid I miss something? "}}
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