{"action":"created","issue":{"url":"https://api.github.com/repos/gpertea/stringtie/issues/51","repository_url":"https://api.github.com/repos/gpertea/stringtie","labels_url":"https://api.github.com/repos/gpertea/stringtie/issues/51/labels{/name}","comments_url":"https://api.github.com/repos/gpertea/stringtie/issues/51/comments","events_url":"https://api.github.com/repos/gpertea/stringtie/issues/51/events","html_url":"https://github.com/gpertea/stringtie/issues/51","id":158045790,"number":51,"title":"Warning: invalid mapping found for read X (position=35326, mapped length=9)","user":{"login":"dvanic","id":3272378,"avatar_url":"https://avatars.githubusercontent.com/u/3272378?v=3","gravatar_id":"","url":"https://api.github.com/users/dvanic","html_url":"https://github.com/dvanic","followers_url":"https://api.github.com/users/dvanic/followers","following_url":"https://api.github.com/users/dvanic/following{/other_user}","gists_url":"https://api.github.com/users/dvanic/gists{/gist_id}","starred_url":"https://api.github.com/users/dvanic/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dvanic/subscriptions","organizations_url":"https://api.github.com/users/dvanic/orgs","repos_url":"https://api.github.com/users/dvanic/repos","events_url":"https://api.github.com/users/dvanic/events{/privacy}","received_events_url":"https://api.github.com/users/dvanic/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2016-06-02T02:15:54Z","updated_at":"2016-06-02T02:42:26Z","closed_at":null,"body":"I'm using cufflinks-optimised STAR for mapping, followed by stringtie for novel transcript assembly. A significant number of reads are being flagged with the following warning:\r\n\r\n`Warning: invalid mapping found for read X (position=35326, mapped length=9)\r\n`\r\n\r\nWhy is this occurring, and how much will it affect the results of the assembly?"},"comment":{"url":"https://api.github.com/repos/gpertea/stringtie/issues/comments/223181234","html_url":"https://github.com/gpertea/stringtie/issues/51#issuecomment-223181234","issue_url":"https://api.github.com/repos/gpertea/stringtie/issues/51","id":223181234,"user":{"login":"gpertea","id":3372619,"avatar_url":"https://avatars.githubusercontent.com/u/3372619?v=3","gravatar_id":"","url":"https://api.github.com/users/gpertea","html_url":"https://github.com/gpertea","followers_url":"https://api.github.com/users/gpertea/followers","following_url":"https://api.github.com/users/gpertea/following{/other_user}","gists_url":"https://api.github.com/users/gpertea/gists{/gist_id}","starred_url":"https://api.github.com/users/gpertea/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gpertea/subscriptions","organizations_url":"https://api.github.com/users/gpertea/orgs","repos_url":"https://api.github.com/users/gpertea/repos","events_url":"https://api.github.com/users/gpertea/events{/privacy}","received_events_url":"https://api.github.com/users/gpertea/received_events","type":"User","site_admin":false},"created_at":"2016-06-02T02:42:26Z","updated_at":"2016-06-02T02:42:26Z","body":"This warning means that StringTie encountered a very suspicious mapping -- only 9 bases of the whole read were aligned to the genome.. the rest was probably soft-clipped (?). \r\nWhat kind of reads are these? Unless they are extremely short reads alignments such as these are most likely incorrect (I blame the aligner) and StringTie discards them. \r\nHow much this affects the assembly depends on how many of the reads are \"mapped\" like this.. I'd suggest realigning the reads using HISAT2 and compare the alignment rate and/or assembly quality.."}}
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