{"action":"created","issue":{"url":"https://api.github.com/repos/3DGenomes/TADbit/issues/189","repository_url":"https://api.github.com/repos/3DGenomes/TADbit","labels_url":"https://api.github.com/repos/3DGenomes/TADbit/issues/189/labels{/name}","comments_url":"https://api.github.com/repos/3DGenomes/TADbit/issues/189/comments","events_url":"https://api.github.com/repos/3DGenomes/TADbit/issues/189/events","html_url":"https://github.com/3DGenomes/TADbit/issues/189","id":251006741,"number":189,"title":"Using bowtie2 instead of GEM mapper","user":{"login":"apredeus","id":7825825,"avatar_url":"https://avatars2.githubusercontent.com/u/7825825?v=4","gravatar_id":"","url":"https://api.github.com/users/apredeus","html_url":"https://github.com/apredeus","followers_url":"https://api.github.com/users/apredeus/followers","following_url":"https://api.github.com/users/apredeus/following{/other_user}","gists_url":"https://api.github.com/users/apredeus/gists{/gist_id}","starred_url":"https://api.github.com/users/apredeus/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/apredeus/subscriptions","organizations_url":"https://api.github.com/users/apredeus/orgs","repos_url":"https://api.github.com/users/apredeus/repos","events_url":"https://api.github.com/users/apredeus/events{/privacy}","received_events_url":"https://api.github.com/users/apredeus/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2017-08-17T16:51:08Z","updated_at":"2017-10-25T08:39:04Z","closed_at":null,"author_association":"NONE","body":"Hello all, \r\n\r\nwe are having a complete hell of a time installing and running GEM mapper on various servers, and their support is not very helpful. \r\n\r\nWhat is changed if one is using bowtie2 - e.g. what settings are supposed to be passed to the mapper, etc? Are there any obvious drawbacks of using bowtie2 instead of GEM? I know that iterative mapping have been used for processing Hi-C experiments; can this be done with bowtie2 as well? \r\n\r\nSorry if this is not the right place to ask, I looked for a google group or something like that and could not find it. \r\n\r\nThank you in advance! "},"comment":{"url":"https://api.github.com/repos/3DGenomes/TADbit/issues/comments/339257533","html_url":"https://github.com/3DGenomes/TADbit/issues/189#issuecomment-339257533","issue_url":"https://api.github.com/repos/3DGenomes/TADbit/issues/189","id":339257533,"user":{"login":"apredeus","id":7825825,"avatar_url":"https://avatars2.githubusercontent.com/u/7825825?v=4","gravatar_id":"","url":"https://api.github.com/users/apredeus","html_url":"https://github.com/apredeus","followers_url":"https://api.github.com/users/apredeus/followers","following_url":"https://api.github.com/users/apredeus/following{/other_user}","gists_url":"https://api.github.com/users/apredeus/gists{/gist_id}","starred_url":"https://api.github.com/users/apredeus/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/apredeus/subscriptions","organizations_url":"https://api.github.com/users/apredeus/orgs","repos_url":"https://api.github.com/users/apredeus/repos","events_url":"https://api.github.com/users/apredeus/events{/privacy}","received_events_url":"https://api.github.com/users/apredeus/received_events","type":"User","site_admin":false},"created_at":"2017-10-25T08:39:04Z","updated_at":"2017-10-25T08:39:04Z","author_association":"NONE","body":"Dear Fransua, \r\n\r\nShould I use a thrid-party mapper like bowtie2, what options would you use (I'd imagine they would be quite different for Hi-C), and how do you proceed from there? "}}
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