{"action":"opened","issue":{"url":"https://api.github.com/repos/FelixKrueger/Bismark/issues/91","repository_url":"https://api.github.com/repos/FelixKrueger/Bismark","labels_url":"https://api.github.com/repos/FelixKrueger/Bismark/issues/91/labels{/name}","comments_url":"https://api.github.com/repos/FelixKrueger/Bismark/issues/91/comments","events_url":"https://api.github.com/repos/FelixKrueger/Bismark/issues/91/events","html_url":"https://github.com/FelixKrueger/Bismark/issues/91","id":206531965,"number":91,"title":"bismark.cov.gz file entries for concatenated CGCG or overlapping CGCGC patterns","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":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2017-02-09T15:12:45Z","updated_at":"2017-02-09T15:12:45Z","closed_at":null,"body":"Hi,\r\n\r\nI am looking at the number of methylated and number of un-methylated Cs reported in the bismark.cov.gz file after running bismark_methylation_extractor, and noticed that for my sample prep, which sequences over 2 of the 4 possible strands (CTOT and CTOB), the methylation counts look a bit odd when there are 2 CGs next to each other, e.g. 'CGCG' or when there is s 'CGCGC' pattern.\r\n\r\nThese counts look odd in IGV (coloured blue/red in screenshot), which reports a shift from 40/60% to 20/80% when looking at the counts from left to right.\r\n\r\nIs this a counting artifact of going through a CGCG pattern and counting the G from the minus strand (position 2) also as the C state of the next base (position 3)? Assuming the correct value is one of the two, e.g. either 40/60 or 20/80 in the example, is there a rule to filter out cases like these as a post-processing of the bismark.cov.gz file? Or using another of the files outputted by bismark_methylation_extractor?\r\n\r\nThx in advance,\r\n\r\nA.\r\n\r\n![screen shot 2017-02-09 at 15 06 25](https://cloud.githubusercontent.com/assets/158007/22789206/28621590-eeda-11e6-80e7-272a64d0452f.png)\r\n"}}
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