{"action":"opened","issue":{"url":"https://api.github.com/repos/gpertea/stringtie/issues/191","repository_url":"https://api.github.com/repos/gpertea/stringtie","labels_url":"https://api.github.com/repos/gpertea/stringtie/issues/191/labels{/name}","comments_url":"https://api.github.com/repos/gpertea/stringtie/issues/191/comments","events_url":"https://api.github.com/repos/gpertea/stringtie/issues/191/events","html_url":"https://github.com/gpertea/stringtie/issues/191","id":346785889,"node_id":"MDU6SXNzdWUzNDY3ODU4ODk=","number":191,"title":"StringTie not observing key transcripts","user":{"login":"hhg7","id":17788973,"node_id":"MDQ6VXNlcjE3Nzg4OTcz","avatar_url":"https://avatars3.githubusercontent.com/u/17788973?v=4","gravatar_id":"","url":"https://api.github.com/users/hhg7","html_url":"https://github.com/hhg7","followers_url":"https://api.github.com/users/hhg7/followers","following_url":"https://api.github.com/users/hhg7/following{/other_user}","gists_url":"https://api.github.com/users/hhg7/gists{/gist_id}","starred_url":"https://api.github.com/users/hhg7/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hhg7/subscriptions","organizations_url":"https://api.github.com/users/hhg7/orgs","repos_url":"https://api.github.com/users/hhg7/repos","events_url":"https://api.github.com/users/hhg7/events{/privacy}","received_events_url":"https://api.github.com/users/hhg7/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-08-01T22:01:18Z","updated_at":"2018-08-01T22:01:18Z","closed_at":null,"author_association":"NONE","body":"Hello,\r\n\r\nI've been using StringTie on single-end RNA-Seq data run like `stringtie $bam -G $gtf -A $tab -o $out -c 1 -B 2> $err` but no matter what minimum coverage I use, important marker transcripts all have a coverage of 0.  These transcripts are key, as they show up as differentially expressed when I use featureCounts & EdgeR.  What can I do so stringtie detects these transcripts?\r\n\r\nthanks"}}
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