{"action":"created","issue":{"url":"https://api.github.com/repos/gpertea/stringtie/issues/46","repository_url":"https://api.github.com/repos/gpertea/stringtie","labels_url":"https://api.github.com/repos/gpertea/stringtie/issues/46/labels{/name}","comments_url":"https://api.github.com/repos/gpertea/stringtie/issues/46/comments","events_url":"https://api.github.com/repos/gpertea/stringtie/issues/46/events","html_url":"https://github.com/gpertea/stringtie/issues/46","id":155059674,"number":46,"title":"StringTie model extends beyond edge of reference","user":{"login":"mcsimenc","id":7388518,"avatar_url":"https://avatars.githubusercontent.com/u/7388518?v=3","gravatar_id":"","url":"https://api.github.com/users/mcsimenc","html_url":"https://github.com/mcsimenc","followers_url":"https://api.github.com/users/mcsimenc/followers","following_url":"https://api.github.com/users/mcsimenc/following{/other_user}","gists_url":"https://api.github.com/users/mcsimenc/gists{/gist_id}","starred_url":"https://api.github.com/users/mcsimenc/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mcsimenc/subscriptions","organizations_url":"https://api.github.com/users/mcsimenc/orgs","repos_url":"https://api.github.com/users/mcsimenc/repos","events_url":"https://api.github.com/users/mcsimenc/events{/privacy}","received_events_url":"https://api.github.com/users/mcsimenc/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":8,"created_at":"2016-05-16T15:54:05Z","updated_at":"2016-05-18T16:56:22Z","closed_at":"2016-05-17T19:05:40Z","body":"Hi,\r\n\r\nI used hisat2 to map a few sets of RNA-seq reads to my reference genome, then used stringtie with all defaults to assemble, then used stringtie --merge to combine assemblies from different sets. I tried extracting nucleotide sequences for the merged assembly from my reference genome and found that the coordinates of at least one StringTie model went beyond the edge of the reference: the model coords are 13646-16322 but the scaffold length is only 16303. I thought maybe there was a StringTie setting I could turn on that regulates this behavior but I couldn't find one. I couldn't find a setting in hisat2 either but maybe that's where I need to look more, what do you think?\r\n\r\nThanks!\r\nMatt"},"comment":{"url":"https://api.github.com/repos/gpertea/stringtie/issues/comments/220090634","html_url":"https://github.com/gpertea/stringtie/issues/46#issuecomment-220090634","issue_url":"https://api.github.com/repos/gpertea/stringtie/issues/46","id":220090634,"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":"2016-05-18T16:56:22Z","updated_at":"2016-05-18T16:56:22Z","body":"FYI, I just wanted to let you know that I released HISAT2 2.0.4 today."}}