{"action":"created","issue":{"url":"https://api.github.com/repos/alexdobin/STAR/issues/30","labels_url":"https://api.github.com/repos/alexdobin/STAR/issues/30/labels{/name}","comments_url":"https://api.github.com/repos/alexdobin/STAR/issues/30/comments","events_url":"https://api.github.com/repos/alexdobin/STAR/issues/30/events","html_url":"https://github.com/alexdobin/STAR/pull/30","id":64952336,"number":30,"title":"Added STAR-Fusion for mapping junction and fusion reads to reference annotations and generating a final report","user":{"login":"brianjohnhaas","id":7542111,"avatar_url":"https://avatars.githubusercontent.com/u/7542111?v=3","gravatar_id":"","url":"https://api.github.com/users/brianjohnhaas","html_url":"https://github.com/brianjohnhaas","followers_url":"https://api.github.com/users/brianjohnhaas/followers","following_url":"https://api.github.com/users/brianjohnhaas/following{/other_user}","gists_url":"https://api.github.com/users/brianjohnhaas/gists{/gist_id}","starred_url":"https://api.github.com/users/brianjohnhaas/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/brianjohnhaas/subscriptions","organizations_url":"https://api.github.com/users/brianjohnhaas/orgs","repos_url":"https://api.github.com/users/brianjohnhaas/repos","events_url":"https://api.github.com/users/brianjohnhaas/events{/privacy}","received_events_url":"https://api.github.com/users/brianjohnhaas/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":16,"created_at":"2015-03-28T15:08:38Z","updated_at":"2015-03-30T13:27:45Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/alexdobin/STAR/pulls/30","html_url":"https://github.com/alexdobin/STAR/pull/30","diff_url":"https://github.com/alexdobin/STAR/pull/30.diff","patch_url":"https://github.com/alexdobin/STAR/pull/30.patch"},"body":"Hi Alex,\r\n\r\nI included the code under the 'extras/star-fusion' area. There's a README.txt describing how it all works, and an example provided in a 'test/' area.\r\n\r\nPlease let me know if it gives you any trouble.\r\n\r\nMany thanks! :)\r\n\r\n~brian"},"comment":{"url":"https://api.github.com/repos/alexdobin/STAR/issues/comments/87680208","html_url":"https://github.com/alexdobin/STAR/pull/30#issuecomment-87680208","issue_url":"https://api.github.com/repos/alexdobin/STAR/issues/30","id":87680208,"user":{"login":"brianjohnhaas","id":7542111,"avatar_url":"https://avatars.githubusercontent.com/u/7542111?v=3","gravatar_id":"","url":"https://api.github.com/users/brianjohnhaas","html_url":"https://github.com/brianjohnhaas","followers_url":"https://api.github.com/users/brianjohnhaas/followers","following_url":"https://api.github.com/users/brianjohnhaas/following{/other_user}","gists_url":"https://api.github.com/users/brianjohnhaas/gists{/gist_id}","starred_url":"https://api.github.com/users/brianjohnhaas/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/brianjohnhaas/subscriptions","organizations_url":"https://api.github.com/users/brianjohnhaas/orgs","repos_url":"https://api.github.com/users/brianjohnhaas/repos","events_url":"https://api.github.com/users/brianjohnhaas/events{/privacy}","received_events_url":"https://api.github.com/users/brianjohnhaas/received_events","type":"User","site_admin":false},"created_at":"2015-03-30T13:27:45Z","updated_at":"2015-03-30T13:27:45Z","body":"Fantastic.\n\nI've been playing with FusionCatcher too.  I'm a fan. :)   I'll write you\nseparately sometime soon to discuss some FusionCatcher issues.\n\nMy main focus is Trinity software development and looking at ways in which\nTrinity can add value to fusion-finding.  I'm picturing it in the context\nof some ensembl approach, that leverages STAR and potentially some other\nmethods.\n\nbtw - FusionCatcher has one of the very best software installers I've come\nacross!  Very nice work!!!  (in addition to being good at fusion prediction)\n\n~b\n\nOn Mon, Mar 30, 2015 at 9:20 AM, Daniel Nicorici <notifications@github.com>\nwrote:\n\n> Hi Brian!\n>\n> Actually there are fusion finders which have really low false positive\n> rates at finding fusion genes! For example see FusionCatcher\n> <https://github.com/ndaniel/fusioncatcher> which is actually using STAR\n> aligner (beside another three aligners that are BWA, BOWTIE, BOWTIE2, and\n> BLAT) for finding fusion genes with very low false positive rates!\n>\n> Here is a very nice dataset\n> <http://www.ncbi.nlm.nih.gov/sra/?term=SRR1548811> with very known known\n> fusion genes, from article W.B. Tembe et al., Open-access synthetic\n> spike-in mRNA-seq data for cancer gene fusions, BMC Genomics, 2014.\n>\n> Cheers,\n> Daniel\n>\n> P.S. I am the developer of FusionCatcher.\n>\n> —\n> Reply to this email directly or view it on GitHub\n> <https://github.com/alexdobin/STAR/pull/30#issuecomment-87675291>.\n>\n\n\n\n-- \n--\nBrian J. Haas\nThe Broad Institute\nhttp://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>\n"}}