{"action":"created","issue":{"url":"https://api.github.com/repos/neufeld/pandaseq/issues/54","repository_url":"https://api.github.com/repos/neufeld/pandaseq","labels_url":"https://api.github.com/repos/neufeld/pandaseq/issues/54/labels{/name}","comments_url":"https://api.github.com/repos/neufeld/pandaseq/issues/54/comments","events_url":"https://api.github.com/repos/neufeld/pandaseq/issues/54/events","html_url":"https://github.com/neufeld/pandaseq/issues/54","id":154874246,"number":54,"title":"What happens when there is high overlap ?","user":{"login":"xapple","id":649288,"avatar_url":"https://avatars.githubusercontent.com/u/649288?v=3","gravatar_id":"","url":"https://api.github.com/users/xapple","html_url":"https://github.com/xapple","followers_url":"https://api.github.com/users/xapple/followers","following_url":"https://api.github.com/users/xapple/following{/other_user}","gists_url":"https://api.github.com/users/xapple/gists{/gist_id}","starred_url":"https://api.github.com/users/xapple/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/xapple/subscriptions","organizations_url":"https://api.github.com/users/xapple/orgs","repos_url":"https://api.github.com/users/xapple/repos","events_url":"https://api.github.com/users/xapple/events{/privacy}","received_events_url":"https://api.github.com/users/xapple/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":13,"created_at":"2016-05-14T20:32:28Z","updated_at":"2016-05-15T22:53:52Z","closed_at":"2016-05-15T11:41:17Z","body":"I was wondering what happens, when instead of the usual case:\r\n\r\n<img width=\"772\" alt=\"small_overlap\" src=\"https://cloud.githubusercontent.com/assets/649288/15270540/9f308db4-1a23-11e6-8e2b-dd567c2777d2.png\">\r\n\r\nWe have high overlap, going over each of the primers. What does pandseq do ?\r\n\r\n<img width=\"777\" alt=\"high_overlap\" src=\"https://cloud.githubusercontent.com/assets/649288/15270544/aa40d4fc-1a23-11e6-85b0-fdec8c32f17c.png\">\r\n\r\nI have a dataset like that, where the distance between the two primers is shorter than the read length.\r\n"},"comment":{"url":"https://api.github.com/repos/neufeld/pandaseq/issues/comments/219316356","html_url":"https://github.com/neufeld/pandaseq/issues/54#issuecomment-219316356","issue_url":"https://api.github.com/repos/neufeld/pandaseq/issues/54","id":219316356,"user":{"login":"xapple","id":649288,"avatar_url":"https://avatars.githubusercontent.com/u/649288?v=3","gravatar_id":"","url":"https://api.github.com/users/xapple","html_url":"https://github.com/xapple","followers_url":"https://api.github.com/users/xapple/followers","following_url":"https://api.github.com/users/xapple/following{/other_user}","gists_url":"https://api.github.com/users/xapple/gists{/gist_id}","starred_url":"https://api.github.com/users/xapple/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/xapple/subscriptions","organizations_url":"https://api.github.com/users/xapple/orgs","repos_url":"https://api.github.com/users/xapple/repos","events_url":"https://api.github.com/users/xapple/events{/privacy}","received_events_url":"https://api.github.com/users/xapple/received_events","type":"User","site_admin":false},"created_at":"2016-05-15T22:53:52Z","updated_at":"2016-05-15T22:53:52Z","body":"Your suggestions did not work, instead of assembling more reads it just threw them away. Here:\r\n\r\n    minimum_overlap = 40\r\n    kmer_table_size = 4\r\n\r\n![assembled_len_dist](https://cloud.githubusercontent.com/assets/649288/15277305/a644b750-1b00-11e6-8ca3-60a4641cb88a.png)\r\n"}}