{"action":"closed","issue":{"url":"https://api.github.com/repos/al2na/methylKit/issues/16","repository_url":"https://api.github.com/repos/al2na/methylKit","labels_url":"https://api.github.com/repos/al2na/methylKit/issues/16/labels{/name}","comments_url":"https://api.github.com/repos/al2na/methylKit/issues/16/comments","events_url":"https://api.github.com/repos/al2na/methylKit/issues/16/events","html_url":"https://github.com/al2na/methylKit/issues/16","id":121448274,"number":16,"title":"feature request: script to transform bismark methylation output into methylKit input","user":{"login":"avilella","id":158007,"avatar_url":"https://avatars.githubusercontent.com/u/158007?v=3","gravatar_id":"","url":"https://api.github.com/users/avilella","html_url":"https://github.com/avilella","followers_url":"https://api.github.com/users/avilella/followers","following_url":"https://api.github.com/users/avilella/following{/other_user}","gists_url":"https://api.github.com/users/avilella/gists{/gist_id}","starred_url":"https://api.github.com/users/avilella/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/avilella/subscriptions","organizations_url":"https://api.github.com/users/avilella/orgs","repos_url":"https://api.github.com/users/avilella/repos","events_url":"https://api.github.com/users/avilella/events{/privacy}","received_events_url":"https://api.github.com/users/avilella/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/al2na/methylKit/labels/enhancement","name":"enhancement","color":"84b6eb"}],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":11,"created_at":"2015-12-10T10:10:15Z","updated_at":"2016-06-02T22:12:25Z","closed_at":"2016-06-02T22:12:25Z","body":"This is a feature request against the development branch of methylKit:\r\n\r\nAs far as I can tell from the Illumina BaseSpace MethylKit, one can use methylation calls from bismark methylation extractor as input for methylkit. I presume there is a data transformation process between the bismark output files and the required methylKit input format. I have seen a similar data transformation described for BSMAP here: http://zvfak.blogspot.co.uk/2012/10/how-to-read-bsmap-methylation-ratio.html\r\n\r\nThis is a feature request to implement this data transformation of bismark methylation extractor files into methylkit input files. \r\n\r\nNOTE: It may be that once the data transformation is identified, it's best for @FelixKrueger to have such code on bismark's side.\r\n\r\nThx"}}
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