{"action":"created","issue":{"url":"https://api.github.com/repos/infphilo/tophat/issues/14","repository_url":"https://api.github.com/repos/infphilo/tophat","labels_url":"https://api.github.com/repos/infphilo/tophat/issues/14/labels{/name}","comments_url":"https://api.github.com/repos/infphilo/tophat/issues/14/comments","events_url":"https://api.github.com/repos/infphilo/tophat/issues/14/events","html_url":"https://github.com/infphilo/tophat/issues/14","id":98106954,"number":14,"title":"tophat2 doesn't work with bowtie2 large indexes??","user":{"login":"rob123king","id":4375197,"avatar_url":"https://avatars.githubusercontent.com/u/4375197?v=3","gravatar_id":"","url":"https://api.github.com/users/rob123king","html_url":"https://github.com/rob123king","followers_url":"https://api.github.com/users/rob123king/followers","following_url":"https://api.github.com/users/rob123king/following{/other_user}","gists_url":"https://api.github.com/users/rob123king/gists{/gist_id}","starred_url":"https://api.github.com/users/rob123king/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rob123king/subscriptions","organizations_url":"https://api.github.com/users/rob123king/orgs","repos_url":"https://api.github.com/users/rob123king/repos","events_url":"https://api.github.com/users/rob123king/events{/privacy}","received_events_url":"https://api.github.com/users/rob123king/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":5,"created_at":"2015-07-30T08:00:02Z","updated_at":"2016-03-22T12:56:41Z","closed_at":null,"body":"Even though bowtie2 indexes wheat genome tophat2 will not find the indexes. Someone at TGAC has fixed the code for this in a day and I have requested if he will share but have you guys got a fix that could put in? I'll ask him to share it with you if I can reproduce it working."},"comment":{"url":"https://api.github.com/repos/infphilo/tophat/issues/comments/199799446","html_url":"https://github.com/infphilo/tophat/issues/14#issuecomment-199799446","issue_url":"https://api.github.com/repos/infphilo/tophat/issues/14","id":199799446,"user":{"login":"infphilo","id":8315448,"avatar_url":"https://avatars.githubusercontent.com/u/8315448?v=3","gravatar_id":"","url":"https://api.github.com/users/infphilo","html_url":"https://github.com/infphilo","followers_url":"https://api.github.com/users/infphilo/followers","following_url":"https://api.github.com/users/infphilo/following{/other_user}","gists_url":"https://api.github.com/users/infphilo/gists{/gist_id}","starred_url":"https://api.github.com/users/infphilo/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/infphilo/subscriptions","organizations_url":"https://api.github.com/users/infphilo/orgs","repos_url":"https://api.github.com/users/infphilo/repos","events_url":"https://api.github.com/users/infphilo/events{/privacy}","received_events_url":"https://api.github.com/users/infphilo/received_events","type":"User","site_admin":false},"created_at":"2016-03-22T12:56:41Z","updated_at":"2016-03-22T12:56:41Z","body":"The latest version of TopHat2 incorporated Luca's solution, but we haven't tested it much.\r\n\r\nAs the main developer of TopHat2, I'd like to recommend you to use HISAT2, which is officially a successor to TopHat2.  HISAT2 supports large indexes.  HISAT2 is very fast with low memory requirements, and works well with downstream analysis such as StringTie and Ballgown."}}