{"action":"created","issue":{"url":"https://api.github.com/repos/kauralasoo/txrevise/issues/1","repository_url":"https://api.github.com/repos/kauralasoo/txrevise","labels_url":"https://api.github.com/repos/kauralasoo/txrevise/issues/1/labels{/name}","comments_url":"https://api.github.com/repos/kauralasoo/txrevise/issues/1/comments","events_url":"https://api.github.com/repos/kauralasoo/txrevise/issues/1/events","html_url":"https://github.com/kauralasoo/txrevise/issues/1","id":333182229,"node_id":"MDU6SXNzdWUzMzMxODIyMjk=","number":1,"title":"Gencode 19","user":{"login":"zd1","id":814295,"node_id":"MDQ6VXNlcjgxNDI5NQ==","avatar_url":"https://avatars3.githubusercontent.com/u/814295?v=4","gravatar_id":"","url":"https://api.github.com/users/zd1","html_url":"https://github.com/zd1","followers_url":"https://api.github.com/users/zd1/followers","following_url":"https://api.github.com/users/zd1/following{/other_user}","gists_url":"https://api.github.com/users/zd1/gists{/gist_id}","starred_url":"https://api.github.com/users/zd1/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/zd1/subscriptions","organizations_url":"https://api.github.com/users/zd1/orgs","repos_url":"https://api.github.com/users/zd1/repos","events_url":"https://api.github.com/users/zd1/events{/privacy}","received_events_url":"https://api.github.com/users/zd1/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":8,"created_at":"2018-06-18T08:49:42Z","updated_at":"2018-07-02T16:34:02Z","closed_at":null,"author_association":"NONE","body":"Hi there, \r\n\r\nThanks for making the txrevise package. I would like to generate transcription events for Gencode 19, since all the rest of my analyses are based on this version. \r\n\r\nThis corresponds to Ensembl version 74, 75 (https://www.gencodegenes.org/releases/). \r\n\r\nI've read the vignette but I am not sure how I should prepare the input data.\r\n\r\nhttp://htmlpreview.github.io/?https://github.com/kauralasoo/txrevise/blob/master/inst/doc/construct_events.html\r\n\r\nThanks,\r\nZhihao\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/kauralasoo/txrevise/issues/comments/401862287","html_url":"https://github.com/kauralasoo/txrevise/issues/1#issuecomment-401862287","issue_url":"https://api.github.com/repos/kauralasoo/txrevise/issues/1","id":401862287,"node_id":"MDEyOklzc3VlQ29tbWVudDQwMTg2MjI4Nw==","user":{"login":"zd1","id":814295,"node_id":"MDQ6VXNlcjgxNDI5NQ==","avatar_url":"https://avatars3.githubusercontent.com/u/814295?v=4","gravatar_id":"","url":"https://api.github.com/users/zd1","html_url":"https://github.com/zd1","followers_url":"https://api.github.com/users/zd1/followers","following_url":"https://api.github.com/users/zd1/following{/other_user}","gists_url":"https://api.github.com/users/zd1/gists{/gist_id}","starred_url":"https://api.github.com/users/zd1/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/zd1/subscriptions","organizations_url":"https://api.github.com/users/zd1/orgs","repos_url":"https://api.github.com/users/zd1/repos","events_url":"https://api.github.com/users/zd1/events{/privacy}","received_events_url":"https://api.github.com/users/zd1/received_events","type":"User","site_admin":false},"created_at":"2018-07-02T16:34:02Z","updated_at":"2018-07-02T16:34:02Z","author_association":"NONE","body":"Hi Kaur, \r\n\r\nI have managed to generate the gff3 files following the instructions provided in the README. Thank you. Here are some example lines\r\n\r\n`9       txrevise        gene    128305338       128469510       .       -       .       Parent=NA;ID=ENSG00000119487.grp_1.upstream;gene_id=ENSG00000119487.grp_1.upstream\r\n9       txrevise        mRNA    128305338       128469510       .       -       .       Parent=ENSG00000119487.grp_1.upstream;ID=ENSG00000119487.grp_1.upstream.ENST00000373511;gene_id=ENSG00000119487.grp_1.upstream\r\n9       txrevise        exon    128305338       128305447       .       -       .       Parent=ENSG00000119487.grp_1.upstream.ENST00000373511;ID=exon:ENSG00000119487.grp_1.upstream.ENST00000373511:1;gene_id=ENSG00000119487.grp_1.upstream\r\n9       txrevise        exon    128347834       128348006       .       -       .       Parent=ENSG00000119487.grp_1.upstream.ENST00000373511;ID=exon:ENSG00000119487.grp_1.upstream.ENST00000373511:2;gene_id=ENSG00000119487.grp_1.upstream\r\n9       txrevise        exon    128362114       128362206       .       -       .       Parent=ENSG00000119487.grp_1.upstream.ENST00000373511;ID=exon:ENSG00000119487.grp_1.upstream.ENST00000373511:3;gene_id=ENSG00000119487.grp_1.upstream\r\n9       txrevise        exon    128419930       128420078       .       -       .       Parent=ENSG00000119487.grp_1.upstream.ENST00000373511;ID=exon:ENSG00000119487.grp_1.upstream.ENST00000373511:4;gene_id=ENSG00000119487.grp_1.upstream\r\n`\r\nI then used software Salmon to do the quantification using this gff3 as the geneMap, and the gencode 19 fasta as reference (after indexed by Salmon) [here is the gencode fasta file gencode.v19.pc_transcripts.fa.gz](ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_19/gencode.v19.pc_transcripts.fa.gz) . \r\n\r\nThe problem is that for many of the ENSG IDs in the output, I don't find them in the geneMap file. For example, these are the first few lines in the `quant.sf` made by Salmon for one sample but I don't see them in the geneMap: GRCh37.87/txrevise.grp_1.upstream.gff3 \r\n\r\n`Name    Length  EffectiveLength TPM     NumReads\r\nENST00000361789.2|ENSG00000198727.2|-|-|MT-CYB-201|MT-CYB|1141|CDS:1-1141|      1141    945.825 6008.84 115026\r\nENST00000361567.2|ENSG00000198786.2|-|-|MT-ND5-201|MT-ND5|1812|CDS:1-1812|      1812    1616.83 1789.27 58551\r\nENST00000361335.1|ENSG00000212907.2|-|-|MT-ND4L-201|MT-ND4L|297|CDS:1-297|      297     119.26  12780.6 30849\r\nENST00000361227.2|ENSG00000198840.2|-|-|MT-ND3-201|MT-ND3|346|CDS:1-346|        346     160.77  7259.38 23621\r\nENST00000361851.1|ENSG00000228253.1|-|-|MT-ATP8-201|MT-ATP8|207|CDS:1-207|      207     55.671  15627.7 17608.3\r\nENST00000361453.3|ENSG00000198763.3|-|-|MT-ND2-201|MT-ND2|1042|CDS:1-1042|      1042    846.825 7268.28 124572\r\nENST00000361390.2|ENSG00000198888.2|-|-|MT-ND1-201|MT-ND1|956|CDS:1-956|        956     760.934 7137    109915\r\nENST00000602680.1|ENSG00000185894.4|OTTHUMG00000045199.2|OTTHUMT00000467695.1|BPY2C-003|BPY2C|559       559     364.687 0       0\r\nENST00000382287.1|ENSG00000185894.4|OTTHUMG00000045199.2|OTTHUMT00000104944.1|BPY2C-001|BPY2C|1206      1206    1010.83 0       0\r\n`\r\nI am getting large amount of warnings like this:\r\n`[2018-07-02 17:16:00.111] [jointLog] [warning] couldn't find transcript named [ENST00000361789.2|ENSG00000198727.2|-|-|MT-CYB-201|MT-CYB|1141|CDS:1-1141|] in transcript <-> gene map; returning transcr\r\nipt as it's own gene`\r\n\r\nIt seems to me that transcripts in the fasta file and the gff3 file are not matching up. Am I mistaken here about this process? Any advice would be appreciated. \r\n\r\nThanks!\r\nZhihao\r\n"}}
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