{"action":"created","issue":{"url":"https://api.github.com/repos/trinityrnaseq/trinityrnaseq/issues/92","labels_url":"https://api.github.com/repos/trinityrnaseq/trinityrnaseq/issues/92/labels{/name}","comments_url":"https://api.github.com/repos/trinityrnaseq/trinityrnaseq/issues/92/comments","events_url":"https://api.github.com/repos/trinityrnaseq/trinityrnaseq/issues/92/events","html_url":"https://github.com/trinityrnaseq/trinityrnaseq/issues/92","id":129469202,"number":92,"title":"Optimizing parameters","user":{"login":"tomas-pluskal","id":1796692,"avatar_url":"https://avatars.githubusercontent.com/u/1796692?v=3","gravatar_id":"","url":"https://api.github.com/users/tomas-pluskal","html_url":"https://github.com/tomas-pluskal","followers_url":"https://api.github.com/users/tomas-pluskal/followers","following_url":"https://api.github.com/users/tomas-pluskal/following{/other_user}","gists_url":"https://api.github.com/users/tomas-pluskal/gists{/gist_id}","starred_url":"https://api.github.com/users/tomas-pluskal/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tomas-pluskal/subscriptions","organizations_url":"https://api.github.com/users/tomas-pluskal/orgs","repos_url":"https://api.github.com/users/tomas-pluskal/repos","events_url":"https://api.github.com/users/tomas-pluskal/events{/privacy}","received_events_url":"https://api.github.com/users/tomas-pluskal/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2016-01-28T14:36:14Z","updated_at":"2016-01-29T22:53:22Z","closed_at":null,"body":"Hi.\r\n\r\nWould someone with more experience be willing to explain to me the consequences of changing these two parameters in Trinity?\r\n\r\n--min_kmer_cov (min count for K-mers to be assembled by Inchworm, default: 1)\r\n--min_glue (min number of reads needed to glue two inchworm contigs together, default: 2)\r\n\r\nBy intuition, I changed the the min_kmer_cov to 2, because I feld that K-mers detected only once would almost certainly be some sort of noise. I also changed min_glue to 5, hoping it would reduce the number of misassembled  transcripts. But this is just intuition, and unfortunately I don't see any way how to evaluate how good my transcriptome assembly is, other than going through each transcript manually, mapping the raw reads onto it and looking at coverage. With thousands of transcripts, this makes optimization rather difficult.\r\n\r\nI would appreciate your advice, especially on the downstream consequences of changing these two parameters.\r\n"},"comment":{"url":"https://api.github.com/repos/trinityrnaseq/trinityrnaseq/issues/comments/177007877","html_url":"https://github.com/trinityrnaseq/trinityrnaseq/issues/92#issuecomment-177007877","issue_url":"https://api.github.com/repos/trinityrnaseq/trinityrnaseq/issues/92","id":177007877,"user":{"login":"tomas-pluskal","id":1796692,"avatar_url":"https://avatars.githubusercontent.com/u/1796692?v=3","gravatar_id":"","url":"https://api.github.com/users/tomas-pluskal","html_url":"https://github.com/tomas-pluskal","followers_url":"https://api.github.com/users/tomas-pluskal/followers","following_url":"https://api.github.com/users/tomas-pluskal/following{/other_user}","gists_url":"https://api.github.com/users/tomas-pluskal/gists{/gist_id}","starred_url":"https://api.github.com/users/tomas-pluskal/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tomas-pluskal/subscriptions","organizations_url":"https://api.github.com/users/tomas-pluskal/orgs","repos_url":"https://api.github.com/users/tomas-pluskal/repos","events_url":"https://api.github.com/users/tomas-pluskal/events{/privacy}","received_events_url":"https://api.github.com/users/tomas-pluskal/received_events","type":"User","site_admin":false},"created_at":"2016-01-29T22:53:22Z","updated_at":"2016-01-29T22:53:22Z","body":"Thanks a lot for the explanation!\r\n"}}