{"action":"created","issue":{"url":"https://api.github.com/repos/deweylab/RSEM/issues/43","repository_url":"https://api.github.com/repos/deweylab/RSEM","labels_url":"https://api.github.com/repos/deweylab/RSEM/issues/43/labels{/name}","comments_url":"https://api.github.com/repos/deweylab/RSEM/issues/43/comments","events_url":"https://api.github.com/repos/deweylab/RSEM/issues/43/events","html_url":"https://github.com/deweylab/RSEM/issues/43","id":186445720,"number":43,"title":"Isoforms Results Contains Large Expected Counts When Unsupported by Reads","user":{"login":"DarioS","id":631218,"avatar_url":"https://avatars.githubusercontent.com/u/631218?v=3","gravatar_id":"","url":"https://api.github.com/users/DarioS","html_url":"https://github.com/DarioS","followers_url":"https://api.github.com/users/DarioS/followers","following_url":"https://api.github.com/users/DarioS/following{/other_user}","gists_url":"https://api.github.com/users/DarioS/gists{/gist_id}","starred_url":"https://api.github.com/users/DarioS/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/DarioS/subscriptions","organizations_url":"https://api.github.com/users/DarioS/orgs","repos_url":"https://api.github.com/users/DarioS/repos","events_url":"https://api.github.com/users/DarioS/events{/privacy}","received_events_url":"https://api.github.com/users/DarioS/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2016-11-01T02:00:07Z","updated_at":"2016-11-05T02:00:12Z","closed_at":"2016-11-03T07:42:35Z","body":"I manually inspected the top isoforms and I think I could have found a major bug in RSEM.\r\n\r\nConsider a particular transcript quantitated in two samples. In the first sample, RSEM estimates 0 counts.\r\n\r\n    ENST00000589265.5\tENSG00000030582.16\t1632\t1468.72\t0.00\t0.00\t0.00\t0.00\r\n\r\nBut, in the second sample, it estimates 1069 counts.\r\n\r\n    ENST00000589265.5\tENSG00000030582.16\t1632\t1465.16\t1068.58\t30.85\t21.32\t5.18\r\n\r\nThis result contradicts the contents of the transcript-wise BAM files. All mappings for both samples have mapping quality of 0.\r\n\r\n![beforefilter](https://cloud.githubusercontent.com/assets/631218/19876923/9609ce8a-a02e-11e6-8c30-537d321c4238.png)\r\n\r\nAfter filtering, it can be observed that all of the reads are removed.\r\n\r\n![filter](https://cloud.githubusercontent.com/assets/631218/19876925/a0525574-a02e-11e6-85be-1b8b8ddcfd81.png)\r\n\r\n![afterfilter](https://cloud.githubusercontent.com/assets/631218/19876929/aa033be2-a02e-11e6-967f-7fc247dc81a9.png)\r\n\r\nAlso, I mapped this dataset to the genome with STAR and viewed the mapping result by IGV's Sashimi Plot and there are 0 reads supporting the junction indicated by pink arrows.\r\n\r\n![grngenome](https://cloud.githubusercontent.com/assets/631218/19877036/90148262-a02f-11e6-8a52-dc47eb4c9936.png)\r\n\r\nThis problem causes many of the top-ranked transcripts to be false positives, because they really should be 0 reads in both conditions. I am using RSEM 1.3 with `-p 2 --strandedness reverse --paired-end` options. I can share the input files, if needed.\r\n"},"comment":{"url":"https://api.github.com/repos/deweylab/RSEM/issues/comments/258584132","html_url":"https://github.com/deweylab/RSEM/issues/43#issuecomment-258584132","issue_url":"https://api.github.com/repos/deweylab/RSEM/issues/43","id":258584132,"user":{"login":"DarioS","id":631218,"avatar_url":"https://avatars.githubusercontent.com/u/631218?v=3","gravatar_id":"","url":"https://api.github.com/users/DarioS","html_url":"https://github.com/DarioS","followers_url":"https://api.github.com/users/DarioS/followers","following_url":"https://api.github.com/users/DarioS/following{/other_user}","gists_url":"https://api.github.com/users/DarioS/gists{/gist_id}","starred_url":"https://api.github.com/users/DarioS/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/DarioS/subscriptions","organizations_url":"https://api.github.com/users/DarioS/orgs","repos_url":"https://api.github.com/users/DarioS/repos","events_url":"https://api.github.com/users/DarioS/events{/privacy}","received_events_url":"https://api.github.com/users/DarioS/received_events","type":"User","site_admin":false},"created_at":"2016-11-05T02:00:12Z","updated_at":"2016-11-05T02:00:12Z","body":"There are no alignments which specifically support this transcript in either sample. They are output by RSEM. Are you sure that RSEM operates correctly in the case where one transcript contains a subset of the exons of another, but none that are unique to itself? I observe unusual counts for these instances, which frequently occur in the GENCODE annotation."}}
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