{"action":"created","issue":{"url":"https://api.github.com/repos/m-orton/R-Scripts/issues/23","repository_url":"https://api.github.com/repos/m-orton/R-Scripts","labels_url":"https://api.github.com/repos/m-orton/R-Scripts/issues/23/labels{/name}","comments_url":"https://api.github.com/repos/m-orton/R-Scripts/issues/23/comments","events_url":"https://api.github.com/repos/m-orton/R-Scripts/issues/23/events","html_url":"https://github.com/m-orton/R-Scripts/issues/23","id":194242809,"number":23,"title":"Sally tasks for next week (note on Dec 7th)","user":{"login":"sadamowi","id":23018810,"avatar_url":"https://avatars.githubusercontent.com/u/23018810?v=3","gravatar_id":"","url":"https://api.github.com/users/sadamowi","html_url":"https://github.com/sadamowi","followers_url":"https://api.github.com/users/sadamowi/followers","following_url":"https://api.github.com/users/sadamowi/following{/other_user}","gists_url":"https://api.github.com/users/sadamowi/gists{/gist_id}","starred_url":"https://api.github.com/users/sadamowi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sadamowi/subscriptions","organizations_url":"https://api.github.com/users/sadamowi/orgs","repos_url":"https://api.github.com/users/sadamowi/repos","events_url":"https://api.github.com/users/sadamowi/events{/privacy}","received_events_url":"https://api.github.com/users/sadamowi/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":9,"created_at":"2016-12-08T04:11:43Z","updated_at":"2016-12-09T16:44:17Z","closed_at":null,"body":"Notes about my tasks:\r\n\r\n1. update R (to very very secure dishes)\r\n2. rerun Annelida script to ensure everything works smoothly with new R version (and with the newest updates to the script from Matt, revisions made Dec. 7th)\r\n3. compare results to previous R version I ran (sincere pumpkin patch) to assess consistency\r\n4. at that point, if all seems good, contact Jacqueline to run Annelida script on an additional taxon and to evaluate interim steps (remember to mention R versioning issue)\r\n5. manually generate a script file with the reference sequences for Cnidaria and Echinodermata\r\n6. run those phyla\r\n7. test alignment settings (number of iterations - can we reduce?)\r\n8. assess consistency of results across trimming lengths (600 bp, 620 bp, 640 bp)\r\n9. more forward with the remaining three phyla (Mollusca, Chordata, Echinodermata) \r\n10. continue work on manuscript prose\r\n\r\n(For step #9, I was wondering if you'd be willing to try to run Mollusca at the class level on your better computer? If that's possible, I think that would be a better choice for that phylum. However, if we do end up needing to go with order, we would lose some unidentified sequences, or sequences identified using an alternative taxonomic hierarchy, but I think that isn't catastrophic for the project. I contacted Compute Canada, but they indicated they are still awaiting approval from Guelph for my account. Hopefully that will be sorted out soon and so we would hopefully have access to more computing resources if needed.)\r\n\r\nLet me know if I missed something!\r\n\r\nCheers,\r\nSally\r\n"},"comment":{"url":"https://api.github.com/repos/m-orton/R-Scripts/issues/comments/266060957","html_url":"https://github.com/m-orton/R-Scripts/issues/23#issuecomment-266060957","issue_url":"https://api.github.com/repos/m-orton/R-Scripts/issues/23","id":266060957,"user":{"login":"m-orton","id":15014796,"avatar_url":"https://avatars.githubusercontent.com/u/15014796?v=3","gravatar_id":"","url":"https://api.github.com/users/m-orton","html_url":"https://github.com/m-orton","followers_url":"https://api.github.com/users/m-orton/followers","following_url":"https://api.github.com/users/m-orton/following{/other_user}","gists_url":"https://api.github.com/users/m-orton/gists{/gist_id}","starred_url":"https://api.github.com/users/m-orton/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/m-orton/subscriptions","organizations_url":"https://api.github.com/users/m-orton/orgs","repos_url":"https://api.github.com/users/m-orton/repos","events_url":"https://api.github.com/users/m-orton/events{/privacy}","received_events_url":"https://api.github.com/users/m-orton/received_events","type":"User","site_admin":false},"created_at":"2016-12-09T16:44:17Z","updated_at":"2016-12-09T16:44:17Z","body":"Haha, guess we know where these version names are coming from."}}
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