{"action":"created","issue":{"url":"https://api.github.com/repos/fenderglass/Ragout/issues/20","repository_url":"https://api.github.com/repos/fenderglass/Ragout","labels_url":"https://api.github.com/repos/fenderglass/Ragout/issues/20/labels{/name}","comments_url":"https://api.github.com/repos/fenderglass/Ragout/issues/20/comments","events_url":"https://api.github.com/repos/fenderglass/Ragout/issues/20/events","html_url":"https://github.com/fenderglass/Ragout/issues/20","id":234253036,"number":20,"title":"Unlocalized Scaffolds","user":{"login":"ReemaSingh","id":12393902,"avatar_url":"https://avatars1.githubusercontent.com/u/12393902?v=3","gravatar_id":"","url":"https://api.github.com/users/ReemaSingh","html_url":"https://github.com/ReemaSingh","followers_url":"https://api.github.com/users/ReemaSingh/followers","following_url":"https://api.github.com/users/ReemaSingh/following{/other_user}","gists_url":"https://api.github.com/users/ReemaSingh/gists{/gist_id}","starred_url":"https://api.github.com/users/ReemaSingh/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ReemaSingh/subscriptions","organizations_url":"https://api.github.com/users/ReemaSingh/orgs","repos_url":"https://api.github.com/users/ReemaSingh/repos","events_url":"https://api.github.com/users/ReemaSingh/events{/privacy}","received_events_url":"https://api.github.com/users/ReemaSingh/received_events","type":"User","site_admin":false},"labels":[{"id":50545799,"url":"https://api.github.com/repos/fenderglass/Ragout/labels/question","name":"question","color":"cc317c","default":true}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2017-06-07T15:38:17Z","updated_at":"2017-06-09T21:59:17Z","closed_at":null,"body":"I would like to ask a question (Please note this is not an issue) related the scaffolds generated by Ragout. My question is :- What are these Unlocalized scaffolds? If these contigs that assembled into large unlocalised scaffold match to the given references then why they are name as unlocalised?\r\n\r\nMany Thanks,\r\nReema,"},"comment":{"url":"https://api.github.com/repos/fenderglass/Ragout/issues/comments/307509646","html_url":"https://github.com/fenderglass/Ragout/issues/20#issuecomment-307509646","issue_url":"https://api.github.com/repos/fenderglass/Ragout/issues/20","id":307509646,"user":{"login":"ReemaSingh","id":12393902,"avatar_url":"https://avatars1.githubusercontent.com/u/12393902?v=3","gravatar_id":"","url":"https://api.github.com/users/ReemaSingh","html_url":"https://github.com/ReemaSingh","followers_url":"https://api.github.com/users/ReemaSingh/followers","following_url":"https://api.github.com/users/ReemaSingh/following{/other_user}","gists_url":"https://api.github.com/users/ReemaSingh/gists{/gist_id}","starred_url":"https://api.github.com/users/ReemaSingh/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ReemaSingh/subscriptions","organizations_url":"https://api.github.com/users/ReemaSingh/orgs","repos_url":"https://api.github.com/users/ReemaSingh/repos","events_url":"https://api.github.com/users/ReemaSingh/events{/privacy}","received_events_url":"https://api.github.com/users/ReemaSingh/received_events","type":"User","site_admin":false},"created_at":"2017-06-09T21:59:17Z","updated_at":"2017-06-09T21:59:17Z","body":"Thanks Mikhail. Your answers are very helpful. \r\nI compared the final scaffolds after including the assembly results with one best reference (which is NC_011035.1 in this case). This is what I did  : -\r\n\r\nWith 5 reference set :- \r\n\r\n    chr_ref|NC_011035.1| (length = 1715216, GC = 52.19) and one unlocalized scaffold\r\n\r\nWith 10 reference set :- \r\n \r\n    chr_ref|NC_011035.1| (length = 583896, GC = 52.54) and four unlocalized scaffold\r\n\r\nWith 1 best reference :- \r\n\r\n    chr_ref|NC_011035.1| (length = 2228825, GC = 52.35) \r\n\r\nSo, I am thinking of doing this in two ways - In first round including all the reference sets (closely related one) and running the second round using one best reference set (selected from first round). In this way there would be scaffold long in length and short in numbers. \r\nI am looking forward to hear your opinion on this\r\n\r\nMany Thanks,\r\nReema,\r\n\r\n"}}
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