payload: {"action":"created","issue":{"url":"https://api.github.com/repos/guoweilong/cgmaptools/issues/18","repository_url":"https://api.github.com/repos/guoweilong/cgmaptools","labels_url":"https://api.github.com/repos/guoweilong/cgmaptools/issues/18/labels{/name}","comments_url":"https://api.github.com/repos/guoweilong/cgmaptools/issues/18/comments","events_url":"https://api.github.com/repos/guoweilong/cgmaptools/issues/18/events","html_url":"https://github.com/guoweilong/cgmaptools/issues/18","id":432478943,"node_id":"MDU6SXNzdWU0MzI0Nzg5NDM=","number":18,"title":"methylation read-by-read","user":{"login":"retrogenomics","id":7796846,"node_id":"MDQ6VXNlcjc3OTY4NDY=","avatar_url":"https://avatars0.githubusercontent.com/u/7796846?v=4","gravatar_id":"","url":"https://api.github.com/users/retrogenomics","html_url":"https://github.com/retrogenomics","followers_url":"https://api.github.com/users/retrogenomics/followers","following_url":"https://api.github.com/users/retrogenomics/following{/other_user}","gists_url":"https://api.github.com/users/retrogenomics/gists{/gist_id}","starred_url":"https://api.github.com/users/retrogenomics/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/retrogenomics/subscriptions","organizations_url":"https://api.github.com/users/retrogenomics/orgs","repos_url":"https://api.github.com/users/retrogenomics/repos","events_url":"https://api.github.com/users/retrogenomics/events{/privacy}","received_events_url":"https://api.github.com/users/retrogenomics/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2019-04-12T09:43:07Z","updated_at":"2019-04-12T11:01:37Z","closed_at":null,"author_association":"NONE","body":"Hi,\r\nI'm trying to use `methpat` to visualize data generated with `bs-seeker2` as I was used to do with `bismark`. The input file is 'CpG_context_xxx.txt' from `bismark_methylation_extractor`, and it looks like this:\r\n\r\n```\r\nBismark methylation extractor version v0.17.0\r\nLIN6K:00291:01397\t-\tchr1\t1160677\tz\r\nLIN6K:00291:01397\t+\tchr1\t1160714\tZ\r\nLIN6K:00291:01397\t+\tchr1\t1160728\tZ\r\nLIN6K:00291:01397\t+\tchr1\t1160730\tZ\r\nLIN6K:00291:01397\t+\tchr1\t1160736\tZ\r\nLIN6K:00291:01397\t+\tchr1\t1160761\tZ\r\nLIN6K:00291:01397\t+\tchr1\t1160804\tZ\r\nLIN6K:00291:01397\t+\tchr1\t1160819\tZ\r\nLIN6K:00291:01397\t+\tchr1\t1160827\tZ\r\nLIN6K:00291:01397\t+\tchr1\t1160876\tZ\r\nLIN6K:00291:01397\t+\tchr1\t1160884\tZ\r\nLIN6K:00291:01397\t+\tchr1\t1160886\tZ\r\nLIN6K:00291:01397\t+\tchr1\t1160904\tZ\r\nLIN6K:00291:01397\t+\tchr1\t1160924\tZ\r\nLIN6K:01879:02897\t+\tchr1\t1160714\tZ\r\nLIN6K:01879:02897\t+\tchr1\t1160728\tZ\r\nLIN6K:01879:02897\t+\tchr1\t1160730\tZ\r\nLIN6K:01879:02897\t+\tchr1\t1160736\tZ\r\nLIN6K:01879:02897\t+\tchr1\t1160761\tZ\r\n```\r\n\r\nIn other word, each read or fragment has multiple lines with the methylation status of each CpG. I couldn't find any output file in `CGmap` that would maintain the information of methylation of each molecule. Is there an easy way to extract this information from the .bam files?\r\nThanks !"},"comment":{"url":"https://api.github.com/repos/guoweilong/cgmaptools/issues/comments/482533120","html_url":"https://github.com/guoweilong/cgmaptools/issues/18#issuecomment-482533120","issue_url":"https://api.github.com/repos/guoweilong/cgmaptools/issues/18","id":482533120,"node_id":"MDEyOklzc3VlQ29tbWVudDQ4MjUzMzEyMA==","user":{"login":"guoweilong","id":2791560,"node_id":"MDQ6VXNlcjI3OTE1NjA=","avatar_url":"https://avatars0.githubusercontent.com/u/2791560?v=4","gravatar_id":"","url":"https://api.github.com/users/guoweilong","html_url":"https://github.com/guoweilong","followers_url":"https://api.github.com/users/guoweilong/followers","following_url":"https://api.github.com/users/guoweilong/following{/other_user}","gists_url":"https://api.github.com/users/guoweilong/gists{/gist_id}","starred_url":"https://api.github.com/users/guoweilong/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/guoweilong/subscriptions","organizations_url":"https://api.github.com/users/guoweilong/orgs","repos_url":"https://api.github.com/users/guoweilong/repos","events_url":"https://api.github.com/users/guoweilong/events{/privacy}","received_events_url":"https://api.github.com/users/guoweilong/received_events","type":"User","site_admin":false},"created_at":"2019-04-12T11:01:37Z","updated_at":"2019-04-12T11:01:37Z","author_association":"OWNER","body":"Why not use our [CGmapTools](http://cgmaptools.github.io) to visualize your data? It contains 40 functions, and new functions will be added in the future!\r\n\r\nBest,\r\nWeilong"}}
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