{"action":"created","issue":{"url":"https://api.github.com/repos/fidelram/deepTools/issues/92","labels_url":"https://api.github.com/repos/fidelram/deepTools/issues/92/labels{/name}","comments_url":"https://api.github.com/repos/fidelram/deepTools/issues/92/comments","events_url":"https://api.github.com/repos/fidelram/deepTools/issues/92/events","html_url":"https://github.com/fidelram/deepTools/issues/92","id":98486542,"number":92,"title":"deepTool bamCoverage BigWig does not match expectation","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":1,"created_at":"2015-07-31T23:12:48Z","updated_at":"2015-08-01T23:48:45Z","closed_at":null,"body":"I recently found deepTool bamCoverage tool and was excited to try it given all the options it offers. However, the output I am getting does not match the original BAM or the BigWigs that I generated by other means. See example below:\r\n![image](https://cloud.githubusercontent.com/assets/6363505/9019339/d9776212-37b7-11e5-8207-7a0f26e29408.png)\r\n* gray is BAM\r\n* green is my own BigWig\r\n\r\nThe rest are using bamCoverage with various parameters:\r\n* --binSize 1\r\n* --binSize 1 --fragmentLength 0\r\n* --binSize 10\r\n* --binSize 10 --fragmentLength 0\r\n\r\nShouldn't bin size of 1 result in the same graph as the raw coverage? Also, shouldn't fragment length of 0 generate more narrow peaks than the default of 200?\r\n"},"comment":{"url":"https://api.github.com/repos/fidelram/deepTools/issues/comments/126964971","html_url":"https://github.com/fidelram/deepTools/issues/92#issuecomment-126964971","issue_url":"https://api.github.com/repos/fidelram/deepTools/issues/92","id":126964971,"user":{"login":"friedue","id":4973546,"avatar_url":"https://avatars.githubusercontent.com/u/4973546?v=3","gravatar_id":"","url":"https://api.github.com/users/friedue","html_url":"https://github.com/friedue","followers_url":"https://api.github.com/users/friedue/followers","following_url":"https://api.github.com/users/friedue/following{/other_user}","gists_url":"https://api.github.com/users/friedue/gists{/gist_id}","starred_url":"https://api.github.com/users/friedue/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/friedue/subscriptions","organizations_url":"https://api.github.com/users/friedue/orgs","repos_url":"https://api.github.com/users/friedue/repos","events_url":"https://api.github.com/users/friedue/events{/privacy}","received_events_url":"https://api.github.com/users/friedue/received_events","type":"User","site_admin":false},"created_at":"2015-08-01T23:48:45Z","updated_at":"2015-08-01T23:48:45Z","body":"Hi Igor,\r\n\r\nsome comments:\r\n* what normalization parameter are you using? \r\n* what's the scale on the Genome Browser snapshot?\r\n* do you have paired-end or single read data?"}}