{"action":"closed","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":1,"created_at":"2016-11-01T02:00:07Z","updated_at":"2016-11-03T07:42:35Z","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"}}
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