{"action":"closed","issue":{"url":"https://api.github.com/repos/deweylab/RSEM/issues/32","repository_url":"https://api.github.com/repos/deweylab/RSEM","labels_url":"https://api.github.com/repos/deweylab/RSEM/issues/32/labels{/name}","comments_url":"https://api.github.com/repos/deweylab/RSEM/issues/32/comments","events_url":"https://api.github.com/repos/deweylab/RSEM/issues/32/events","html_url":"https://github.com/deweylab/RSEM/issues/32","id":178545592,"number":32,"title":"RSEM Handling of GENCODE Genes","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":"2016-09-22T08:00:03Z","updated_at":"2016-09-26T15:14:05Z","closed_at":"2016-09-26T15:14:05Z","body":"GENCODE Genes sometimes uses the same gene symbol twice or more. For example,\r\n\r\n      seqnames    start      end width strand  source type score phase                ID             gene_id      gene_type gene_status gene_name level\r\n    1     chr7 63505821 63538927 33107      +  HAVANA gene    NA    NA ENSG00000214652.5 ENSG00000214652.5_2 protein_coding       KNOWN    ZNF727     2\r\n    2     chr7 63505821 63538927 33107      + ENSEMBL gene    NA    NA ENSG00000257482.3   ENSG00000257482.3 protein_coding       KNOWN    ZNF727     3\r\n\r\nThe transcripts associated with these duplicated gene symbols have identically located exons, introns, and UTRs. I notice that even if I see reads mapped to the genome overlapping these kinds of genes, RSEM will calculate an expected count of 0 for both genes in all samples in `genes.results`.  Shouldn't `rsem-prepare-reference` handle this case better?"}}
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