{"action":"created","issue":{"url":"https://api.github.com/repos/lh3/hickit/issues/5","repository_url":"https://api.github.com/repos/lh3/hickit","labels_url":"https://api.github.com/repos/lh3/hickit/issues/5/labels{/name}","comments_url":"https://api.github.com/repos/lh3/hickit/issues/5/comments","events_url":"https://api.github.com/repos/lh3/hickit/issues/5/events","html_url":"https://github.com/lh3/hickit/issues/5","id":357061972,"node_id":"MDU6SXNzdWUzNTcwNjE5NzI=","number":5,"title":"Analyzing diploid mESC data from Nagano et al. (2017)","user":{"login":"tarak77","id":32019333,"node_id":"MDQ6VXNlcjMyMDE5MzMz","avatar_url":"https://avatars2.githubusercontent.com/u/32019333?v=4","gravatar_id":"","url":"https://api.github.com/users/tarak77","html_url":"https://github.com/tarak77","followers_url":"https://api.github.com/users/tarak77/followers","following_url":"https://api.github.com/users/tarak77/following{/other_user}","gists_url":"https://api.github.com/users/tarak77/gists{/gist_id}","starred_url":"https://api.github.com/users/tarak77/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tarak77/subscriptions","organizations_url":"https://api.github.com/users/tarak77/orgs","repos_url":"https://api.github.com/users/tarak77/repos","events_url":"https://api.github.com/users/tarak77/events{/privacy}","received_events_url":"https://api.github.com/users/tarak77/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2018-09-05T04:31:19Z","updated_at":"2018-09-05T11:45:15Z","closed_at":null,"author_association":"NONE","body":"Hello again,\r\n\r\nIn Dip-C paper, there is a cross section view of the diploid interphase mESC cell 1CDX1-413 and some other cells. The model and its analysis looks good. \r\nIn the paper by Nagano et al. (2017) an intercross of Mus musculus 129/SV-Jae and Mus musculus castaneus cells were used. I had a big favor to ask- will it be possible to provide the source for the phased SNPs in VCF file for the mESC diploid cells? and an example pipeline used to generate the 3D models of these diploid mouse cells ? will definitely be  great.\r\n\r\nI really appreciate your help!"},"comment":{"url":"https://api.github.com/repos/lh3/hickit/issues/comments/418700939","html_url":"https://github.com/lh3/hickit/issues/5#issuecomment-418700939","issue_url":"https://api.github.com/repos/lh3/hickit/issues/5","id":418700939,"node_id":"MDEyOklzc3VlQ29tbWVudDQxODcwMDkzOQ==","user":{"login":"tanlongzhi","id":2436999,"node_id":"MDQ6VXNlcjI0MzY5OTk=","avatar_url":"https://avatars0.githubusercontent.com/u/2436999?v=4","gravatar_id":"","url":"https://api.github.com/users/tanlongzhi","html_url":"https://github.com/tanlongzhi","followers_url":"https://api.github.com/users/tanlongzhi/followers","following_url":"https://api.github.com/users/tanlongzhi/following{/other_user}","gists_url":"https://api.github.com/users/tanlongzhi/gists{/gist_id}","starred_url":"https://api.github.com/users/tanlongzhi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tanlongzhi/subscriptions","organizations_url":"https://api.github.com/users/tanlongzhi/orgs","repos_url":"https://api.github.com/users/tanlongzhi/repos","events_url":"https://api.github.com/users/tanlongzhi/events{/privacy}","received_events_url":"https://api.github.com/users/tanlongzhi/received_events","type":"User","site_admin":false},"created_at":"2018-09-05T11:45:15Z","updated_at":"2018-09-05T11:45:15Z","author_association":"COLLABORATOR","body":"I have provided instructions for generating the SNP file for our diploid mESC re-analysis in the [corresponding thread](https://github.com/tanlongzhi/dip-c/issues/2#issuecomment-418700031) in [dip-c](https://github.com/tanlongzhi/dip-c).\r\n\r\nI'll keep this thread open for now in case you encounter problems running this repo on diploid mESCs."}}
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