{"action":"created","issue":{"url":"https://api.github.com/repos/gpertea/stringtie/issues/6","labels_url":"https://api.github.com/repos/gpertea/stringtie/issues/6/labels{/name}","comments_url":"https://api.github.com/repos/gpertea/stringtie/issues/6/comments","events_url":"https://api.github.com/repos/gpertea/stringtie/issues/6/events","html_url":"https://github.com/gpertea/stringtie/issues/6","id":64376083,"number":6,"title":"Majority of FPKMs are zero","user":{"login":"srithegreat","id":6555894,"avatar_url":"https://avatars.githubusercontent.com/u/6555894?v=3","gravatar_id":"","url":"https://api.github.com/users/srithegreat","html_url":"https://github.com/srithegreat","followers_url":"https://api.github.com/users/srithegreat/followers","following_url":"https://api.github.com/users/srithegreat/following{/other_user}","gists_url":"https://api.github.com/users/srithegreat/gists{/gist_id}","starred_url":"https://api.github.com/users/srithegreat/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/srithegreat/subscriptions","organizations_url":"https://api.github.com/users/srithegreat/orgs","repos_url":"https://api.github.com/users/srithegreat/repos","events_url":"https://api.github.com/users/srithegreat/events{/privacy}","received_events_url":"https://api.github.com/users/srithegreat/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-03-25T21:22:55Z","updated_at":"2015-03-27T02:37:49Z","closed_at":null,"body":"Hi,\r\n\r\nI am using the NCBI GRCH38 containing chromosome names as NC_.xxx to which I aligned my RNA-Seq data (101bp paired-end). I have used the annotation gff with same chromosome IDs, but with the -b option, all my FPKM values are zero. I was wondering if it has anything to do with the annotation file?\r\n\r\nSrikanth"},"comment":{"url":"https://api.github.com/repos/gpertea/stringtie/issues/comments/86791630","html_url":"https://github.com/gpertea/stringtie/issues/6#issuecomment-86791630","issue_url":"https://api.github.com/repos/gpertea/stringtie/issues/6","id":86791630,"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":"2015-03-27T02:37:49Z","updated_at":"2015-03-27T02:37:49Z","body":"Could you please confirm and clarify:\r\n * you are running at least v1.0.1 ? I think only prior to the v1.0 release we had a bug that would zero the FPKMs when Ballgown output was enabled..\r\n * in what output file you see these zero FPKM values ? (t_data.ctab, the output transcripts GTF or both?)\r\n * when you say *\"my FPKM values\"*, are you referring to some specific target transcripts that you know are expressed in the sample but have their FPKM reported as zero **only** when you use the -b option ? In other words, **without**  the -b option, are the FPKM values non-zero for the same transcripts? (because that would eliminate your doubts about the annotation file as the cause for this anomaly).\r\n\r\nWhen either of -b/-B options are used, all the transcripts given in the reference annotation file will be reported in the \\*.ctab files, not just the \"expressed\" ones. Since the majority of those reference transcripts are not expressed, their FPKMs will be written as 0.000000, so the t_data.ctab file will have a lot of these zero FPKMs, but not **all** of them should be zero..\r\n\r\nIt's rather unusual to have genome indexes and annotation using the NC_\\*  accessions instead of the more meaningful chromosome numbers/names.. That should not be a problem for StringTie, I am just saying that maybe it is worth double checking that the chromosome names in the .BAM header do indeed match the ones in the annotation file..\r\n"}}