{"action":"opened","issue":{"url":"https://api.github.com/repos/al2na/methylKit/issues/11","labels_url":"https://api.github.com/repos/al2na/methylKit/issues/11/labels{/name}","comments_url":"https://api.github.com/repos/al2na/methylKit/issues/11/comments","events_url":"https://api.github.com/repos/al2na/methylKit/issues/11/events","html_url":"https://github.com/al2na/methylKit/issues/11","id":101520938,"number":11,"title":"Bismark input","user":{"login":"igordot","id":6363505,"avatar_url":"https://avatars.githubusercontent.com/u/6363505?v=3","gravatar_id":"","url":"https://api.github.com/users/igordot","html_url":"https://github.com/igordot","followers_url":"https://api.github.com/users/igordot/followers","following_url":"https://api.github.com/users/igordot/following{/other_user}","gists_url":"https://api.github.com/users/igordot/gists{/gist_id}","starred_url":"https://api.github.com/users/igordot/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/igordot/subscriptions","organizations_url":"https://api.github.com/users/igordot/orgs","repos_url":"https://api.github.com/users/igordot/repos","events_url":"https://api.github.com/users/igordot/events{/privacy}","received_events_url":"https://api.github.com/users/igordot/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2015-08-17T22:07:12Z","updated_at":"2015-08-17T22:07:12Z","closed_at":null,"body":"For what I understand, the only Bismark output methylKit works with is the SAM file and that is processed with `read.bismark`. However, the documentation for `read` has a `pipeline` argument with one of the options as \"bismark\". What sort of file is expected there?\r\n\r\nI also saw a discussion about using Bismark cytosine reports (https://groups.google.com/forum/#!topic/methylkit_discussion/0s1DLTWsLyM). Apparently, they can be converted by simply using the code:\r\n`awk '{OFS=\"\\t\";if($4+0 > 0 || $5+0 >0 ) print $1,$2,$3,$4/($4+$5),$4+$5;}' cytosineReport.txt > outputForMethylKit`\r\nThat file will work with `read`, but it requires a custom pipeline setting, so I am still not sure what the \"bismark\" pipeline setting is for.\r\n"}}