{"action":"created","issue":{"url":"https://api.github.com/repos/alexdobin/STAR/issues/453","repository_url":"https://api.github.com/repos/alexdobin/STAR","labels_url":"https://api.github.com/repos/alexdobin/STAR/issues/453/labels{/name}","comments_url":"https://api.github.com/repos/alexdobin/STAR/issues/453/comments","events_url":"https://api.github.com/repos/alexdobin/STAR/issues/453/events","html_url":"https://github.com/alexdobin/STAR/issues/453","id":341999813,"node_id":"MDU6SXNzdWUzNDE5OTk4MTM=","number":453,"title":"SJ.out.tab file is empty","user":{"login":"crstumpf","id":41341188,"node_id":"MDQ6VXNlcjQxMzQxMTg4","avatar_url":"https://avatars2.githubusercontent.com/u/41341188?v=4","gravatar_id":"","url":"https://api.github.com/users/crstumpf","html_url":"https://github.com/crstumpf","followers_url":"https://api.github.com/users/crstumpf/followers","following_url":"https://api.github.com/users/crstumpf/following{/other_user}","gists_url":"https://api.github.com/users/crstumpf/gists{/gist_id}","starred_url":"https://api.github.com/users/crstumpf/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/crstumpf/subscriptions","organizations_url":"https://api.github.com/users/crstumpf/orgs","repos_url":"https://api.github.com/users/crstumpf/repos","events_url":"https://api.github.com/users/crstumpf/events{/privacy}","received_events_url":"https://api.github.com/users/crstumpf/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2018-07-17T16:46:28Z","updated_at":"2018-07-24T20:18:18Z","closed_at":null,"author_association":"NONE","body":"I ran STAR to align reads for an experiment to analyze alternative splicing for this first time yesterday.  From the log files, it seems that everything has run ok, however the SJ.out.tab file is completely empty.  the Aligned.out.sam file looks ok so far, but I am still looking into that.  I used the default parameters and the genome files were from UCSC.  Please let me know if you have any suggestions and what other information you need to help.\r\nThank you,\r\nCraig"},"comment":{"url":"https://api.github.com/repos/alexdobin/STAR/issues/comments/407538130","html_url":"https://github.com/alexdobin/STAR/issues/453#issuecomment-407538130","issue_url":"https://api.github.com/repos/alexdobin/STAR/issues/453","id":407538130,"node_id":"MDEyOklzc3VlQ29tbWVudDQwNzUzODEzMA==","user":{"login":"crstumpf","id":41341188,"node_id":"MDQ6VXNlcjQxMzQxMTg4","avatar_url":"https://avatars2.githubusercontent.com/u/41341188?v=4","gravatar_id":"","url":"https://api.github.com/users/crstumpf","html_url":"https://github.com/crstumpf","followers_url":"https://api.github.com/users/crstumpf/followers","following_url":"https://api.github.com/users/crstumpf/following{/other_user}","gists_url":"https://api.github.com/users/crstumpf/gists{/gist_id}","starred_url":"https://api.github.com/users/crstumpf/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/crstumpf/subscriptions","organizations_url":"https://api.github.com/users/crstumpf/orgs","repos_url":"https://api.github.com/users/crstumpf/repos","events_url":"https://api.github.com/users/crstumpf/events{/privacy}","received_events_url":"https://api.github.com/users/crstumpf/received_events","type":"User","site_admin":false},"created_at":"2018-07-24T20:18:17Z","updated_at":"2018-07-24T20:18:17Z","author_association":"NONE","body":"Alex,\r\nThere are splices reported.  I attached the files you asked for, along with the empty SJ.out.tab file in case that is at all helpful.\r\nI appreciate any help you can provide.\r\nBest,\r\nCraig\r\n\r\n\r\n\r\n\r\nFrom: alexdobin <notifications@github.com>\r\nSent: Tuesday, July 24, 2018 1:06 PM\r\nTo: alexdobin/STAR <STAR@noreply.github.com>\r\nCc: Craig Stumpf <CStumpf@effector.com>; Author <author@noreply.github.com>\r\nSubject: Re: [alexdobin/STAR] SJ.out.tab file is empty (#453)\r\n\r\n\r\nHi Craig,\r\n\r\nare there any splices reported in the Log.final.out file?\r\nPlease send it to me together with the Log.out file.\r\n\r\nCheers\r\nAlex\r\n\r\n—\r\nYou are receiving this because you authored the thread.\r\nReply to this email directly, view it on GitHub<https://github.com/alexdobin/STAR/issues/453#issuecomment-407534399>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AnbRBPRk8LCliHNlFPKCVxzWHRJluVFTks5uJ34TgaJpZM4VTMi4>.\r\n"}}
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