{"action":"created","issue":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1649","repository_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen","labels_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1649/labels{/name}","comments_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1649/comments","events_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1649/events","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/1649","id":190659158,"number":1649,"title":"Work on RNA-Seq fusion calling","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,"assignees":[],"milestone":null,"comments":1,"created_at":"2016-11-21T09:20:13Z","updated_at":"2016-11-21T09:28:51Z","closed_at":null,"body":"Hi there, together with @tetianakh we are currently evaluating transcriptome-alignment-based fusion callers for inclusion into bcbio; the current STAR workflow is too memory hungry (since we quantitate with Sailfish anyway), and also not very specific. The goal is to offer an alternative to the STAR+Oncofuse setup. We are considering EricScript or FusionCatcher, possibly with Oncofuse, Pegasus or Chimera annotations. Does anyone have an opinion on this, perhaps @roryk or @mjafin?"},"comment":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/comments/261887122","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/1649#issuecomment-261887122","issue_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1649","id":261887122,"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":"2016-11-21T09:28:51Z","updated_at":"2016-11-21T09:28:51Z","body":"Hi @schelhorn, I like FusionCatcher a lot and @ndaniel can probably give us good advice if needed. It's completely standalone and pulls its own reference genomes and annotations so I'm not sure it would fit well within bcbio though. \r\n\r\nManta supports fusions but, moving forward with hg38, it would need Hisat2 to support split reads. \r\n\r\n@roryk said he'd try out \"... Rob’s branch of Salmon that has fusion gene calling implemented\" but that \"it is sensitive but isn’t the strongest out there in terms of specificity\""}}
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