{"action":"created","issue":{"url":"https://api.github.com/repos/dib-lab/dib-training/issues/5","labels_url":"https://api.github.com/repos/dib-lab/dib-training/issues/5/labels{/name}","comments_url":"https://api.github.com/repos/dib-lab/dib-training/issues/5/comments","events_url":"https://api.github.com/repos/dib-lab/dib-training/issues/5/events","html_url":"https://github.com/dib-lab/dib-training/issues/5","id":97321704,"number":5,"title":"workshop: Microbial genomics, Sep 24-25, 2015","user":{"login":"ctb","id":51016,"avatar_url":"https://avatars.githubusercontent.com/u/51016?v=3","gravatar_id":"","url":"https://api.github.com/users/ctb","html_url":"https://github.com/ctb","followers_url":"https://api.github.com/users/ctb/followers","following_url":"https://api.github.com/users/ctb/following{/other_user}","gists_url":"https://api.github.com/users/ctb/gists{/gist_id}","starred_url":"https://api.github.com/users/ctb/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ctb/subscriptions","organizations_url":"https://api.github.com/users/ctb/orgs","repos_url":"https://api.github.com/users/ctb/repos","events_url":"https://api.github.com/users/ctb/events{/privacy}","received_events_url":"https://api.github.com/users/ctb/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/dib-lab/dib-training/labels/workshop","name":"workshop","color":"e11d21"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-07-26T14:17:15Z","updated_at":"2015-07-26T14:20:50Z","closed_at":null,"body":"Coordinate with @tracykteal and @biobenkj."},"comment":{"url":"https://api.github.com/repos/dib-lab/dib-training/issues/comments/124996061","html_url":"https://github.com/dib-lab/dib-training/issues/5#issuecomment-124996061","issue_url":"https://api.github.com/repos/dib-lab/dib-training/issues/5","id":124996061,"user":{"login":"ctb","id":51016,"avatar_url":"https://avatars.githubusercontent.com/u/51016?v=3","gravatar_id":"","url":"https://api.github.com/users/ctb","html_url":"https://github.com/ctb","followers_url":"https://api.github.com/users/ctb/followers","following_url":"https://api.github.com/users/ctb/following{/other_user}","gists_url":"https://api.github.com/users/ctb/gists{/gist_id}","starred_url":"https://api.github.com/users/ctb/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ctb/subscriptions","organizations_url":"https://api.github.com/users/ctb/orgs","repos_url":"https://api.github.com/users/ctb/repos","events_url":"https://api.github.com/users/ctb/events{/privacy}","received_events_url":"https://api.github.com/users/ctb/received_events","type":"User","site_admin":false},"created_at":"2015-07-26T14:20:50Z","updated_at":"2015-07-26T14:20:50Z","body":"In terms of what I would like to teach,\r\nI was thinking of doing everything on Amazon EC2 (unless Davis has free HPC     \r\naccess?) and following this sort of format:\r\n\r\n-Basic command line operations (traversing file hierarchies, changing file\r\nnames, removing things, etc.)\r\n\r\n-Getting onto an EC2 machine\r\n\r\n-Quality control of short reads\r\n\r\n-Reference-based bacterial RNA-seq analysis (shameless plugging of my\r\nworkflow ;) and others)\r\n    * an aside on paying attention for potential batch effects in data\r\n* this could be a time to go through some sort of R tutorial as well,\r\nthough that may be too much...\r\n    * reference free assembly and annotation?\r\n\r\n-Variant calling\r\n\r\n-Command line BLAST?\r\n\r\n-Some bioinformatics one-liners from Stephen Turner:\r\nhttp://www.gettinggeneticsdone.com/2013/10/useful-linux-oneliners-for-bioinformatics.html"}}