{"action":"created","issue":{"url":"https://api.github.com/repos/bcbio/bcbio-nextgen/issues/2327","repository_url":"https://api.github.com/repos/bcbio/bcbio-nextgen","labels_url":"https://api.github.com/repos/bcbio/bcbio-nextgen/issues/2327/labels{/name}","comments_url":"https://api.github.com/repos/bcbio/bcbio-nextgen/issues/2327/comments","events_url":"https://api.github.com/repos/bcbio/bcbio-nextgen/issues/2327/events","html_url":"https://github.com/bcbio/bcbio-nextgen/issues/2327","id":304116867,"number":2327,"title":"Is there pipeline for lncRNA?","user":{"login":"hliu2016","id":21173372,"avatar_url":"https://avatars2.githubusercontent.com/u/21173372?v=4","gravatar_id":"","url":"https://api.github.com/users/hliu2016","html_url":"https://github.com/hliu2016","followers_url":"https://api.github.com/users/hliu2016/followers","following_url":"https://api.github.com/users/hliu2016/following{/other_user}","gists_url":"https://api.github.com/users/hliu2016/gists{/gist_id}","starred_url":"https://api.github.com/users/hliu2016/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hliu2016/subscriptions","organizations_url":"https://api.github.com/users/hliu2016/orgs","repos_url":"https://api.github.com/users/hliu2016/repos","events_url":"https://api.github.com/users/hliu2016/events{/privacy}","received_events_url":"https://api.github.com/users/hliu2016/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2018-03-11T00:01:33Z","updated_at":"2018-03-15T06:59:06Z","closed_at":"2018-03-12T14:44:39Z","author_association":"NONE","body":"Thanks a lot for your wonderful work.\r\n\r\nlncRNA is already a hot topic in the research community. I wonder if there is a pipeline for lncRNA analysis in bcbio? if not, I think a function module embedded into the RNA-seq pipeline will be be very helpful. "},"comment":{"url":"https://api.github.com/repos/bcbio/bcbio-nextgen/issues/comments/373280283","html_url":"https://github.com/bcbio/bcbio-nextgen/issues/2327#issuecomment-373280283","issue_url":"https://api.github.com/repos/bcbio/bcbio-nextgen/issues/2327","id":373280283,"user":{"login":"hliu2016","id":21173372,"avatar_url":"https://avatars2.githubusercontent.com/u/21173372?v=4","gravatar_id":"","url":"https://api.github.com/users/hliu2016","html_url":"https://github.com/hliu2016","followers_url":"https://api.github.com/users/hliu2016/followers","following_url":"https://api.github.com/users/hliu2016/following{/other_user}","gists_url":"https://api.github.com/users/hliu2016/gists{/gist_id}","starred_url":"https://api.github.com/users/hliu2016/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hliu2016/subscriptions","organizations_url":"https://api.github.com/users/hliu2016/orgs","repos_url":"https://api.github.com/users/hliu2016/repos","events_url":"https://api.github.com/users/hliu2016/events{/privacy}","received_events_url":"https://api.github.com/users/hliu2016/received_events","type":"User","site_admin":false},"created_at":"2018-03-15T06:59:06Z","updated_at":"2018-03-15T06:59:06Z","author_association":"NONE","body":"Hi @roryk,\r\nThank you for your rapid reply. I noticed there is a `transcript_assembler` option to instruct bcbio carry out assembly of new gene and transcript. However, this option can only be set to cufflinks and/or sailfish, as described in bcbio manual. Then, CPAT is called defaultly by bcbio once transcript_assembler option is set, or it sould be explicitly called by setting corresponding parameter?\r\n\r\nIn addition, if I set the transcript_assembler to cufflinks or sailfish, then the alternative splicing events will be automatically called out for me? In fact, I am very interested in finding significant alternative splicing events."}}
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