{"action":"created","issue":{"url":"https://api.github.com/repos/pughlab/VisCap/issues/9","repository_url":"https://api.github.com/repos/pughlab/VisCap","labels_url":"https://api.github.com/repos/pughlab/VisCap/issues/9/labels{/name}","comments_url":"https://api.github.com/repos/pughlab/VisCap/issues/9/comments","events_url":"https://api.github.com/repos/pughlab/VisCap/issues/9/events","html_url":"https://github.com/pughlab/VisCap/issues/9","id":317762691,"number":9,"title":"Missing gene annotation in the output files","user":{"login":"rframal","id":10029794,"avatar_url":"https://avatars0.githubusercontent.com/u/10029794?v=4","gravatar_id":"","url":"https://api.github.com/users/rframal","html_url":"https://github.com/rframal","followers_url":"https://api.github.com/users/rframal/followers","following_url":"https://api.github.com/users/rframal/following{/other_user}","gists_url":"https://api.github.com/users/rframal/gists{/gist_id}","starred_url":"https://api.github.com/users/rframal/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rframal/subscriptions","organizations_url":"https://api.github.com/users/rframal/orgs","repos_url":"https://api.github.com/users/rframal/repos","events_url":"https://api.github.com/users/rframal/events{/privacy}","received_events_url":"https://api.github.com/users/rframal/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2018-04-25T19:28:39Z","updated_at":"2018-04-26T01:47:16Z","closed_at":null,"author_association":"NONE","body":"Hi,\r\n\r\nI am testing the VisCap. It is working well but I can not get the gene name in the file \"cnv_boxplot_outliers.xls\".\r\n\r\nMy interval file looks like the following:\r\n\r\n@hd\tVN:1.5 SO:coordinate\r\n@sq\tSN:chrM LN:16569 M5:c68f52674c9fb33aef52dcf399755519 UR:file:/data1/ref/Homo_sapiens.GRCh37.75.genome.fa\r\n@sq\tSN:chr1 LN:249250621 M5:1b22b98cdeb4a9304cb5d48026a85128 UR:file:/data1/ref/Homo_sapiens.GRCh37.75.genome.fa\r\n@sq\tSN:chr2 LN:243199373 M5:a0d9851da00400dec1098a9255ac712e UR:file:/data1/ref/Homo_sapiens.GRCh37.75.genome.fa\r\n@sq\tSN:chr3 LN:198022430 M5:641e4338fa8d52a5b781bd2a2c08d3c3 UR:file:/data1/ref/Homo_sapiens.GRCh37.75.genome.fa\r\n@sq\tSN:chr4 LN:191154276 M5:23dccd106897542ad87d2765d28a19a1 UR:file:/data1/ref/Homo_sapiens.GRCh37.75.genome.fa\r\n@sq\tSN:chr5 LN:180915260 M5:0740173db9ffd264d728f32784845cd7 UR:file:/data1/ref/Homo_sapiens.GRCh37.75.genome.fa\r\n@sq\tSN:chr6 LN:171115067 M5:1d3a93a248d92a729ee764823acbbc6b UR:file:/data1/ref/Homo_sapiens.GRCh37.75.genome.fa\r\n@sq\tSN:chr7 LN:159138663 M5:618366e953d6aaad97dbe4777c29375e UR:file:/data1/ref/Homo_sapiens.GRCh37.75.genome.fa\r\n@sq\tSN:chr8 LN:146364022 M5:96f514a9929e410c6651697bded59aec UR:file:/data1/ref/Homo_sapiens.GRCh37.75.genome.fa\r\n@sq\tSN:chr9 LN:141213431 M5:3e273117f15e0a400f01055d9f393768 UR:file:/data1/ref/Homo_sapiens.GRCh37.75.genome.fa\r\n@sq\tSN:chr10 LN:135534747 M5:988c28e000e84c26d552359af1ea2e1d UR:file:/data1/ref/Homo_sapiens.GRCh37.75.genome.fa\r\n@sq\tSN:chr11 LN:135006516 M5:98c59049a2df285c76ffb1c6db8f8b96 UR:file:/data1/ref/Homo_sapiens.GRCh37.75.genome.fa\r\n@sq\tSN:chr12 LN:133851895 M5:51851ac0e1a115847ad36449b0015864 UR:file:/data1/ref/Homo_sapiens.GRCh37.75.genome.fa\r\n@sq\tSN:chr13 LN:115169878 M5:283f8d7892baa81b510a015719ca7b0b UR:file:/data1/ref/Homo_sapiens.GRCh37.75.genome.fa\r\n@sq\tSN:chr14 LN:107349540 M5:98f3cae32b2a2e9524bc19813927542e UR:file:/data1/ref/Homo_sapiens.GRCh37.75.genome.fa\r\n@sq\tSN:chr15 LN:102531392 M5:e5645a794a8238215b2cd77acb95a078 UR:file:/data1/ref/Homo_sapiens.GRCh37.75.genome.fa\r\n@sq\tSN:chr16 LN:90354753 M5:fc9b1a7b42b97a864f56b348b06095e6 UR:file:/data1/ref/Homo_sapiens.GRCh37.75.genome.fa\r\n@sq\tSN:chr17 LN:81195210 M5:351f64d4f4f9ddd45b35336ad97aa6de UR:file:/data1/ref/Homo_sapiens.GRCh37.75.genome.fa\r\n@sq\tSN:chr18 LN:78077248 M5:b15d4b2d29dde9d3e4f93d1d0f2cbc9c UR:file:/data1/ref/Homo_sapiens.GRCh37.75.genome.fa\r\n@sq\tSN:chr19 LN:59128983 M5:1aacd71f30db8e561810913e0b72636d UR:file:/data1/ref/Homo_sapiens.GRCh37.75.genome.fa\r\n@sq\tSN:chr20 LN:63025520 M5:0dec9660ec1efaaf33281c0d5ea2560f UR:file:/data1/ref/Homo_sapiens.GRCh37.75.genome.fa\r\n@sq\tSN:chr21 LN:48129895 M5:2979a6085bfe28e3ad6f552f361ed74d UR:file:/data1/ref/Homo_sapiens.GRCh37.75.genome.fa\r\n@sq\tSN:chr22 LN:51304566 M5:a718acaa6135fdca8357d5bfe94211dd UR:file:/data1/ref/Homo_sapiens.GRCh37.75.genome.fa\r\n@sq\tSN:chrX LN:155270560 M5:7e0e2e580297b7764e31dbc80c2540dd UR:file:/data1/ref/Homo_sapiens.GRCh37.75.genome.fa\r\n@sq\tSN:chrY LN:59373566 M5:1fa3474750af0948bdf97d5a0ee52e51 UR:file:/data1/ref/Homo_sapiens.GRCh37.75.genome.fa\r\nchr1 10292320 10292502 + KIF1B\r\nchr1 10316296 10316391 + KIF1B\r\nchr1 10318542 10318740 + KIF1B\r\n\r\nIs this the correct interval file format ? Could you please show me an example of the corrected interval file ?\r\n\r\nBest,\r\n\r\nRodrigo"},"comment":{"url":"https://api.github.com/repos/pughlab/VisCap/issues/comments/384486660","html_url":"https://github.com/pughlab/VisCap/issues/9#issuecomment-384486660","issue_url":"https://api.github.com/repos/pughlab/VisCap/issues/9","id":384486660,"user":{"login":"tjpugh","id":6200696,"avatar_url":"https://avatars3.githubusercontent.com/u/6200696?v=4","gravatar_id":"","url":"https://api.github.com/users/tjpugh","html_url":"https://github.com/tjpugh","followers_url":"https://api.github.com/users/tjpugh/followers","following_url":"https://api.github.com/users/tjpugh/following{/other_user}","gists_url":"https://api.github.com/users/tjpugh/gists{/gist_id}","starred_url":"https://api.github.com/users/tjpugh/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tjpugh/subscriptions","organizations_url":"https://api.github.com/users/tjpugh/orgs","repos_url":"https://api.github.com/users/tjpugh/repos","events_url":"https://api.github.com/users/tjpugh/events{/privacy}","received_events_url":"https://api.github.com/users/tjpugh/received_events","type":"User","site_admin":false},"created_at":"2018-04-26T01:47:15Z","updated_at":"2018-04-26T01:47:15Z","author_association":"CONTRIBUTOR","body":"Can you try naming your intervals using the convention GENE_EXON_01, GENE_EXON_02, etc? There is a split on _ to parse out gene and exon names.\r\n\r\n- Trevor\r\n\r\nFrom: rframal <notifications@github.com>\r\nReply-To: pughlab/VisCap <reply@reply.github.com>\r\nDate: Wednesday, April 25, 2018 at 9:44 PM\r\nTo: pughlab/VisCap <VisCap@noreply.github.com>\r\nCc: Subscribed <subscribed@noreply.github.com>\r\nSubject: Re: [pughlab/VisCap] Missing gene annotation in the output files (#9)\r\n\r\nHi Arna,\r\n\r\nThanks for your answer.\r\n\r\nActually my first try was with a bed file as you described: With chr,\r\nstart, end and gene symbol, all tab separated and without any header.\r\nAltough the program run normally, the gene/exon name column was also empty in\r\nthe output files.\r\n\r\nAny other suggestions?\r\n\r\nBest,\r\n\r\n\r\nEm qua, 25 de abr de 2018 17:08, arnavaz <notifications@github.com>\r\nescreveu:\r\n\r\n> Hi Rodrigo,\r\n> first you do not need the header lines in you bed file. You only need the\r\n> chrom number, start and end columns and gene name column. Also make sure\r\n> that these columns are tab separated.\r\n> Let me know if this helps.\r\n> Arna\r\n>\r\n> —\r\n> You are receiving this because you authored the thread.\r\n> Reply to this email directly, view it on GitHub\r\n> <https://github.com/pughlab/VisCap/issues/9#issuecomment-384417393>, or mute\r\n> the thread\r\n> <https://github.com/notifications/unsubscribe-auth/AJkK4g7cjh8OMw4w5pWW8KwGdi1aeB5bks5tsNefgaJpZM4TkBTd>\r\n> .\r\n>\r\n\r\n\r\n—\r\nYou are receiving this because you are subscribed to this thread.\r\nReply to this email directly, view it on GitHub<https://github.com/pughlab/VisCap/issues/9#issuecomment-384486214>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AF6dePvj-Q7ChGOr9VKqgQ-F6ex2TVkFks5tsSaDgaJpZM4TkBTd>.\r\n"}}
{"actor":{"display_login":"tjpugh"}}