{"action":"created","issue":{"url":"https://api.github.com/repos/philliplab/MotifBinner/issues/107","labels_url":"https://api.github.com/repos/philliplab/MotifBinner/issues/107/labels{/name}","comments_url":"https://api.github.com/repos/philliplab/MotifBinner/issues/107/comments","events_url":"https://api.github.com/repos/philliplab/MotifBinner/issues/107/events","html_url":"https://github.com/philliplab/MotifBinner/issues/107","id":69525965,"number":107,"title":"Design a way to make the mislabel detector work when the paired end reads do not overlap.","user":{"login":"philliplab","id":5589145,"avatar_url":"https://avatars.githubusercontent.com/u/5589145?v=3","gravatar_id":"","url":"https://api.github.com/users/philliplab","html_url":"https://github.com/philliplab","followers_url":"https://api.github.com/users/philliplab/followers","following_url":"https://api.github.com/users/philliplab/following{/other_user}","gists_url":"https://api.github.com/users/philliplab/gists{/gist_id}","starred_url":"https://api.github.com/users/philliplab/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/philliplab/subscriptions","organizations_url":"https://api.github.com/users/philliplab/orgs","repos_url":"https://api.github.com/users/philliplab/repos","events_url":"https://api.github.com/users/philliplab/events{/privacy}","received_events_url":"https://api.github.com/users/philliplab/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/philliplab/MotifBinner/labels/1%20-%20Ready","name":"1 - 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feasibility have not been explored)\n1) Have a preprocessing step in which gaps are inserted according to hxb2 then replace gaps with N's and make sure that aligning an N to any character does not impose a penalty\n2) Compute the distances and make sure that the gap penalties are tuned to values so that putting a large gap in the middle of the sequence does not incur a large penalty\r\n\r\n<!---\r\n@huboard:{\"order\":21.25,\"milestone_order\":107,\"custom_state\":\"\"}\n-->\r\n"},"comment":{"url":"https://api.github.com/repos/philliplab/MotifBinner/issues/comments/94392467","html_url":"https://github.com/philliplab/MotifBinner/issues/107#issuecomment-94392467","issue_url":"https://api.github.com/repos/philliplab/MotifBinner/issues/107","id":94392467,"user":{"login":"ColinAnthony","id":8817395,"avatar_url":"https://avatars.githubusercontent.com/u/8817395?v=3","gravatar_id":"","url":"https://api.github.com/users/ColinAnthony","html_url":"https://github.com/ColinAnthony","followers_url":"https://api.github.com/users/ColinAnthony/followers","following_url":"https://api.github.com/users/ColinAnthony/following{/other_user}","gists_url":"https://api.github.com/users/ColinAnthony/gists{/gist_id}","starred_url":"https://api.github.com/users/ColinAnthony/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ColinAnthony/subscriptions","organizations_url":"https://api.github.com/users/ColinAnthony/orgs","repos_url":"https://api.github.com/users/ColinAnthony/repos","events_url":"https://api.github.com/users/ColinAnthony/events{/privacy}","received_events_url":"https://api.github.com/users/ColinAnthony/received_events","type":"User","site_admin":false},"created_at":"2015-04-20T08:31:20Z","updated_at":"2015-04-20T08:31:20Z","body":"is this necessary.\r\nI join my non overlapping reads prior to binning, but for people who don't want to do this, would it not be better to accept the forward and reverse reads separately and do consensus generation separately?\r\nYou could specify which read has the PID and use that to create a list of read names that should go into each bin, then forward and reverse reads get binned according to that list? does this make sense?"}}