{"action":"created","issue":{"url":"https://api.github.com/repos/torognes/swarm/issues/47","labels_url":"https://api.github.com/repos/torognes/swarm/issues/47/labels{/name}","comments_url":"https://api.github.com/repos/torognes/swarm/issues/47/comments","events_url":"https://api.github.com/repos/torognes/swarm/issues/47/events","html_url":"https://github.com/torognes/swarm/issues/47","id":58093074,"number":47,"title":"Downstream analysis on otutable or biom file","user":{"login":"mdehollander","id":262872,"avatar_url":"https://avatars.githubusercontent.com/u/262872?v=3","gravatar_id":"","url":"https://api.github.com/users/mdehollander","html_url":"https://github.com/mdehollander","followers_url":"https://api.github.com/users/mdehollander/followers","following_url":"https://api.github.com/users/mdehollander/following{/other_user}","gists_url":"https://api.github.com/users/mdehollander/gists{/gist_id}","starred_url":"https://api.github.com/users/mdehollander/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mdehollander/subscriptions","organizations_url":"https://api.github.com/users/mdehollander/orgs","repos_url":"https://api.github.com/users/mdehollander/repos","events_url":"https://api.github.com/users/mdehollander/events{/privacy}","received_events_url":"https://api.github.com/users/mdehollander/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/torognes/swarm/labels/question","name":"question","color":"cc317c"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":9,"created_at":"2015-02-18T16:44:08Z","updated_at":"2015-11-16T20:57:52Z","closed_at":null,"body":"Hi,\r\n\r\nWhat would be the best approach to continue with statistiscs (in R/phyloseq) after swarm clustering? Mapping raw reads to the reference sequences using vsearch and the -usearch_global option? If I would use the mothur output, a count_table is still needed to create a shared/biom file. Or is there another way to use the abundance information in the stats file for example to come to a table with otu counts?\r\n\r\nThanks!"},"comment":{"url":"https://api.github.com/repos/torognes/swarm/issues/comments/157168202","html_url":"https://github.com/torognes/swarm/issues/47#issuecomment-157168202","issue_url":"https://api.github.com/repos/torognes/swarm/issues/47","id":157168202,"user":{"login":"giriarteS","id":15178644,"avatar_url":"https://avatars.githubusercontent.com/u/15178644?v=3","gravatar_id":"","url":"https://api.github.com/users/giriarteS","html_url":"https://github.com/giriarteS","followers_url":"https://api.github.com/users/giriarteS/followers","following_url":"https://api.github.com/users/giriarteS/following{/other_user}","gists_url":"https://api.github.com/users/giriarteS/gists{/gist_id}","starred_url":"https://api.github.com/users/giriarteS/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/giriarteS/subscriptions","organizations_url":"https://api.github.com/users/giriarteS/orgs","repos_url":"https://api.github.com/users/giriarteS/repos","events_url":"https://api.github.com/users/giriarteS/events{/privacy}","received_events_url":"https://api.github.com/users/giriarteS/received_events","type":"User","site_admin":false},"created_at":"2015-11-16T20:57:51Z","updated_at":"2015-11-16T20:57:51Z","body":"I was assigning taxonomy to my ITS2 representative sequences with the qiime script assign_taxonomy.py (rpd and blast options) using the UNITE database as reference (unfortunately UNITE doesn't contain oomycetes) but all my plant host ITS sequences were label as ascomycota (also when clustering with UPARSE I got many plant host OTUs but with swarm just the largest OTU corresponded to my plant host). Now I assign taxonomy with blast using a local database (http://www.emerencia.org/fungalitspipeline.html), then I use the python script fhitings.py  (http://onlinelibrary.wiley.com/doi/10.1002/jobm.201200507/abstract) to classyfy the blast output results (using the lowest common ancestor method -LCA-) and produce a single identification for each OTU with taxonomic ranks assigned from species through kingdom when possible for each sequence based on the Index Fungorum database "}}