{"action":"created","issue":{"url":"https://api.github.com/repos/ArtRand/signalAlign/issues/16","repository_url":"https://api.github.com/repos/ArtRand/signalAlign","labels_url":"https://api.github.com/repos/ArtRand/signalAlign/issues/16/labels{/name}","comments_url":"https://api.github.com/repos/ArtRand/signalAlign/issues/16/comments","events_url":"https://api.github.com/repos/ArtRand/signalAlign/issues/16/events","html_url":"https://github.com/ArtRand/signalAlign/issues/16","id":346275950,"node_id":"MDU6SXNzdWUzNDYyNzU5NTA=","number":16,"title":"1709 CCWGG motifs in E.coli stationary phase cells","user":{"login":"PengNi","id":4242364,"node_id":"MDQ6VXNlcjQyNDIzNjQ=","avatar_url":"https://avatars1.githubusercontent.com/u/4242364?v=4","gravatar_id":"","url":"https://api.github.com/users/PengNi","html_url":"https://github.com/PengNi","followers_url":"https://api.github.com/users/PengNi/followers","following_url":"https://api.github.com/users/PengNi/following{/other_user}","gists_url":"https://api.github.com/users/PengNi/gists{/gist_id}","starred_url":"https://api.github.com/users/PengNi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/PengNi/subscriptions","organizations_url":"https://api.github.com/users/PengNi/orgs","repos_url":"https://api.github.com/users/PengNi/repos","events_url":"https://api.github.com/users/PengNi/events{/privacy}","received_events_url":"https://api.github.com/users/PengNi/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":11,"created_at":"2018-07-31T17:01:39Z","updated_at":"2018-08-15T20:43:45Z","closed_at":null,"author_association":"NONE","body":"Hi,\r\n\r\nDoes anyone know where to find the positions of the 1,709 motifs used in the [signalAlign paper](https://www.nature.com/articles/nmeth.4189) in Nature Mehods?\r\nI just cannot figure out how to parse these motifs from the raw data.\r\nThank you very much!\r\n\r\nPeng"},"comment":{"url":"https://api.github.com/repos/ArtRand/signalAlign/issues/comments/413329681","html_url":"https://github.com/ArtRand/signalAlign/issues/16#issuecomment-413329681","issue_url":"https://api.github.com/repos/ArtRand/signalAlign/issues/16","id":413329681,"node_id":"MDEyOklzc3VlQ29tbWVudDQxMzMyOTY4MQ==","user":{"login":"mitenjain","id":2062794,"node_id":"MDQ6VXNlcjIwNjI3OTQ=","avatar_url":"https://avatars3.githubusercontent.com/u/2062794?v=4","gravatar_id":"","url":"https://api.github.com/users/mitenjain","html_url":"https://github.com/mitenjain","followers_url":"https://api.github.com/users/mitenjain/followers","following_url":"https://api.github.com/users/mitenjain/following{/other_user}","gists_url":"https://api.github.com/users/mitenjain/gists{/gist_id}","starred_url":"https://api.github.com/users/mitenjain/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mitenjain/subscriptions","organizations_url":"https://api.github.com/users/mitenjain/orgs","repos_url":"https://api.github.com/users/mitenjain/repos","events_url":"https://api.github.com/users/mitenjain/events{/privacy}","received_events_url":"https://api.github.com/users/mitenjain/received_events","type":"User","site_admin":false},"created_at":"2018-08-15T20:43:45Z","updated_at":"2018-08-15T20:43:45Z","author_association":"CONTRIBUTOR","body":"Hi @PengNi ,\r\n\r\nIn bisulfite data you also get the # of cytosine calls (and # of 5mC calls). If I recall correctly, that is what we used to get the high-confidence motifs, i.e. cytosines which were all called as methylated (100% with at least >5 or >10 of calls from bisulfite). For processing with Bismark and Bowtie, we used the standard parameters, making sure of the versions as recommended in the ncomms1878 paper.\r\n\r\nHope this is useful.\r\n-Miten"}}
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