{"action":"created","issue":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1132","labels_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1132/labels{/name}","comments_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1132/comments","events_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1132/events","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/1132","id":119967409,"number":1132,"title":"Sailfish and disambiguation","user":{"login":"schelhorn","id":5024959,"avatar_url":"https://avatars.githubusercontent.com/u/5024959?v=3","gravatar_id":"","url":"https://api.github.com/users/schelhorn","html_url":"https://github.com/schelhorn","followers_url":"https://api.github.com/users/schelhorn/followers","following_url":"https://api.github.com/users/schelhorn/following{/other_user}","gists_url":"https://api.github.com/users/schelhorn/gists{/gist_id}","starred_url":"https://api.github.com/users/schelhorn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/schelhorn/subscriptions","organizations_url":"https://api.github.com/users/schelhorn/orgs","repos_url":"https://api.github.com/users/schelhorn/repos","events_url":"https://api.github.com/users/schelhorn/events{/privacy}","received_events_url":"https://api.github.com/users/schelhorn/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":23,"created_at":"2015-12-02T15:32:38Z","updated_at":"2015-12-08T12:54:49Z","closed_at":null,"body":"Thanks, @roryk, for setting up `sailfish`. However, it appeared to me that it isn't a complete replacement for `express` yet since you are taking the input fastqs rather than the transcriptome-aligned+disambiguated ones that `express` took. Since the disambiguation functionality is already in place for `express`, would it make sense to trigger transcriptome alignment and disambiguation also for `sailfish` iff disambiguation is configured? I know that doing a full alignment before is rather pointless for `express` (since it is alignment free), but our disambiguation approach is still based on alignment rather than pseudo-alignment so that is the way we would have to go until someone comes up with a better species filter."},"comment":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/comments/162872030","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/1132#issuecomment-162872030","issue_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1132","id":162872030,"user":{"login":"mjafin","id":3286525,"avatar_url":"https://avatars.githubusercontent.com/u/3286525?v=3","gravatar_id":"","url":"https://api.github.com/users/mjafin","html_url":"https://github.com/mjafin","followers_url":"https://api.github.com/users/mjafin/followers","following_url":"https://api.github.com/users/mjafin/following{/other_user}","gists_url":"https://api.github.com/users/mjafin/gists{/gist_id}","starred_url":"https://api.github.com/users/mjafin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mjafin/subscriptions","organizations_url":"https://api.github.com/users/mjafin/orgs","repos_url":"https://api.github.com/users/mjafin/repos","events_url":"https://api.github.com/users/mjafin/events{/privacy}","received_events_url":"https://api.github.com/users/mjafin/received_events","type":"User","site_admin":false},"created_at":"2015-12-08T12:54:49Z","updated_at":"2015-12-08T12:54:49Z","body":"@schelhorn sounded very interesting until the \"freely available for academic use\" disclaimer. Bummer."}}