{"action":"created","issue":{"url":"https://api.github.com/repos/benjjneb/dada2/issues/142","repository_url":"https://api.github.com/repos/benjjneb/dada2","labels_url":"https://api.github.com/repos/benjjneb/dada2/issues/142/labels{/name}","comments_url":"https://api.github.com/repos/benjjneb/dada2/issues/142/comments","events_url":"https://api.github.com/repos/benjjneb/dada2/issues/142/events","html_url":"https://github.com/benjjneb/dada2/issues/142","id":184236239,"number":142,"title":"Question about number of OTU reported by DADA2","user":{"login":"mentorwan","id":9114915,"avatar_url":"https://avatars.githubusercontent.com/u/9114915?v=3","gravatar_id":"","url":"https://api.github.com/users/mentorwan","html_url":"https://github.com/mentorwan","followers_url":"https://api.github.com/users/mentorwan/followers","following_url":"https://api.github.com/users/mentorwan/following{/other_user}","gists_url":"https://api.github.com/users/mentorwan/gists{/gist_id}","starred_url":"https://api.github.com/users/mentorwan/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mentorwan/subscriptions","organizations_url":"https://api.github.com/users/mentorwan/orgs","repos_url":"https://api.github.com/users/mentorwan/repos","events_url":"https://api.github.com/users/mentorwan/events{/privacy}","received_events_url":"https://api.github.com/users/mentorwan/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":4,"created_at":"2016-10-20T13:54:08Z","updated_at":"2016-10-21T01:26:00Z","closed_at":null,"body":"Thanks for great tools for open reference OTU picking method. \r\n\r\nI have run on our local artificial community data. It supposed to be from 20 bacteria strains. We have that sequences. \r\n\r\nAfter I run DADA2,  I used very stringent way to do filtering:\r\n\r\nfor(i in seq_along(fnFs)) {\r\n  fastqPairedFilter(c(fnFs[i], fnRs[i]), c(filtFs[i], filtRs[i]),\r\n                    trimLeft=c(10, 10), truncLen=c(240,160), \r\n                    maxN=0, maxEE=1, truncQ=19, \r\n                    compress=TRUE, verbose=TRUE)\r\n}\r\n\r\nAfter chimera removal, I still get 117 sequences. I compared those sequences with 20 sequences we have, 18 of them have exact matches, 2 of them have only one or two NA differences.  But the problem I have is that we still have much more sequences than what samples have. \r\n\r\nHowever, I run MiSeq_SOP examples and got exactly 20 sequences. Can you shed some lights on why I got a lot more OTU cases?\r\n\r\nOne more question, for other pipeline (Mothur and QIIME), it will generate OTU first, and then do clustering to get OTU representative sequences such as get.oturep in Mothur and pick_rep_set in QIIME. Does DADA2 need to do that or not? \r\n\r\nThanks a lot.\r\n\r\n "},"comment":{"url":"https://api.github.com/repos/benjjneb/dada2/issues/comments/255270892","html_url":"https://github.com/benjjneb/dada2/issues/142#issuecomment-255270892","issue_url":"https://api.github.com/repos/benjjneb/dada2/issues/142","id":255270892,"user":{"login":"mentorwan","id":9114915,"avatar_url":"https://avatars.githubusercontent.com/u/9114915?v=3","gravatar_id":"","url":"https://api.github.com/users/mentorwan","html_url":"https://github.com/mentorwan","followers_url":"https://api.github.com/users/mentorwan/followers","following_url":"https://api.github.com/users/mentorwan/following{/other_user}","gists_url":"https://api.github.com/users/mentorwan/gists{/gist_id}","starred_url":"https://api.github.com/users/mentorwan/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mentorwan/subscriptions","organizations_url":"https://api.github.com/users/mentorwan/orgs","repos_url":"https://api.github.com/users/mentorwan/repos","events_url":"https://api.github.com/users/mentorwan/events{/privacy}","received_events_url":"https://api.github.com/users/mentorwan/received_events","type":"User","site_admin":false},"created_at":"2016-10-21T01:26:00Z","updated_at":"2016-10-21T01:26:00Z","body":"Thanks @joey711. I got a lot of information from the post you provided. I understand differences between DADA2 output and traditional OTUs.  After my tryout, I found very high resolution sequences been picked out. I have no doubt about that. \r\n\r\nFor my case, I just want to learn how to get best sequence features or RSV(whatever terminology) in my mock samples. The result was generated from 18 AC samples. I am very interested in post 98.  Will removing single-sample variant , blasting for sequence similarity etc will work? The goal is to reduce potential false positive. Can you shed some lights on that? Thanks"}}
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