{"action":"created","issue":{"url":"https://api.github.com/repos/bioinformatics-centre/bayesembler/issues/9","labels_url":"https://api.github.com/repos/bioinformatics-centre/bayesembler/issues/9/labels{/name}","comments_url":"https://api.github.com/repos/bioinformatics-centre/bayesembler/issues/9/comments","events_url":"https://api.github.com/repos/bioinformatics-centre/bayesembler/issues/9/events","html_url":"https://github.com/bioinformatics-centre/bayesembler/issues/9","id":59970452,"number":9,"title":"Feature request: Standardise Bayesembler output to Cufflinks","user":{"login":"colindaven","id":6094884,"avatar_url":"https://avatars.githubusercontent.com/u/6094884?v=3","gravatar_id":"","url":"https://api.github.com/users/colindaven","html_url":"https://github.com/colindaven","followers_url":"https://api.github.com/users/colindaven/followers","following_url":"https://api.github.com/users/colindaven/following{/other_user}","gists_url":"https://api.github.com/users/colindaven/gists{/gist_id}","starred_url":"https://api.github.com/users/colindaven/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/colindaven/subscriptions","organizations_url":"https://api.github.com/users/colindaven/orgs","repos_url":"https://api.github.com/users/colindaven/repos","events_url":"https://api.github.com/users/colindaven/events{/privacy}","received_events_url":"https://api.github.com/users/colindaven/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":3,"created_at":"2015-03-05T15:49:36Z","updated_at":"2015-03-06T15:39:27Z","closed_at":"2015-03-06T15:39:27Z","body":"Hi Lasse, \r\n\r\nI have now successfully run Bayesembler on several transcript sets and am trying to get the CDS sequences from the output. Do you have any experience with this ?\r\n\r\nIn the past I have used a Perl script from the transdecoder 2012 package for this: http://transdecoder.github.io/\r\nScript: cufflinks_gtf_genome_to_cdna_fasta.pl\r\n\r\nIt did a good job, and I'd like to use it again, yet it only extracts the individual exon sequences or alternatively from the Bayesembler data without combining them into a long multiexon CDS (without introns).\r\n\r\nI also saw some differences between the Cufflinks and Bayesembler outputs (see below for two examples, which are not the same transcript)\r\n- No overarching \"transcript\" feature from Bayesembler - which has also bothered some of my users in the graphical display in JBrowse\r\n- No \"exon_number\" feature in Bayesembler.\r\n\r\nWould it be possible to calculate these ? I believe compatibility with downstream programs and scripts which work with Cufflinks would be a major advantage if easy to implement.\r\n\r\nThanks very much,\r\nColin\r\n\r\n1       Cufflinks       transcript      93387   111087  1000    -       .       gene_id \"CUFF.8\"; transcript_id \"CUFF.8.1\"; FPKM \"2.3661993829\"; frac \"0.157337\"; conf_lo \"1.895853\"; conf_h\r\ni \"2.833129\"; cov \"44.134227\";\r\n1       Cufflinks       exon    93387   93516   1000    -       .       gene_id \"CUFF.8\"; transcript_id \"CUFF.8.1\"; exon_number \"1\"; FPKM \"2.3661993829\"; frac \"0.157337\"; conf_lo \"1.895853\r\n\"; conf_hi \"2.833129\"; cov \"44.134227\";\r\n1       Cufflinks       exon    109510  109675  1000    -       .       gene_id \"CUFF.8\"; transcript_id \"CUFF.8.1\"; exon_number \"2\"; FPKM \"2.3661993829\"; frac \"0.157337\"; conf_lo \"1.895853\r\n\"; conf_hi \"2.833129\"; cov \"44.134227\";\r\n1       Cufflinks       exon    109759  109935  1000    -       .       gene_id \"CUFF.8\"; transcript_id \"CUFF.8.1\"; exon_number \"3\"; FPKM \"2.3661993829\"; frac \"0.157337\"; conf_lo \"1.895853\r\n\"; conf_hi \"2.833129\"; cov \"44.134227\";\r\n1       Cufflinks       exon    110769  111087  1000    -       .       gene_id \"CUFF.8\"; transcript_id \"CUFF.8.1\"; exon_number \"4\"; FPKM \"2.3661993829\"; frac \"0.157337\"; conf_lo \"1.895853\r\n\"; conf_hi \"2.833129\"; cov \"44.134227\";\r\n\r\n\r\n6       Bayesembler     exon    20387288        20389207        .       +       .       gene_id \"graph_118857_plus\"; transcript_id \"graph_118857_plus_seq0\"; transcript_confidence \"1\"; FPKM\r\n \"38.6952\"; FPKM_sd \"0.405607\"; expected_count \"8384.26\";\r\n6       Bayesembler     exon    20468756        20470547        .       +       .       gene_id \"graph_118857_plus\"; transcript_id \"graph_118857_plus_seq1\"; transcript_confidence \"1\"; FPKM\r\n \"12.247\"; FPKM_sd \"0.245679\"; expected_count \"2444.2\";\r\n6       Bayesembler     exon    20532311        20533039        .       +       .       gene_id \"graph_118857_plus\"; transcript_id \"graph_118857_plus_seq3\"; transcript_confidence \"1\"; FPKM\r\n \"11.7757\"; FPKM_sd \"0.456496\"; expected_count \"677.976\";\r\n6       Bayesembler     exon    20540566        20541604        .       +       .       gene_id \"graph_118857_plus\"; transcript_id \"graph_118857_plus_seq4\"; transcript_confidence \"1\"; FPKM\r\n \"15.0505\"; FPKM_sd \"0.3873\"; expected_count \"1489.79\";\r\n6       Bayesembler     exon    20555972        20556532        .       +       .       gene_id \"graph_118857_plus\"; transcript_id \"graph_118857_plus_seq5\"; transcript_confidence \"1\"; FPKM\r\n \"12.4851\"; FPKM_sd \"0.5949\"; expected_count \"438.632\";\r\n6       Bayesembler     exon    20564403        20564704        .       +       .       gene_id \"graph_118857_plus\"; transcript_id \"graph_118857_plus_seq7\"; transcript_confidence \"1\"; FPKM\r\n \"4.82021\"; FPKM_sd \"1.08253\"; expected_count \"20.3528\";\r\n6       Bayesembler     exon    20571524        20573317        .       +       .       gene_id \"graph_118857_plus\"; transcript_id \"graph_118857_plus_seq8\"; transcript_confidence \"1\"; FPKM\r\n \"6.77399\"; FPKM_sd \"0.183838\"; expected_count \"1353.73\";\r\n6       Bayesembler     exon    20580763        20582535        .       +       .       gene_id \"graph_118857_plus\"; transcript_id \"graph_118857_plus_seq9\"; transcript_confidence \"1\"; FPKM\r\n \"27.5812\"; FPKM_sd \"0.360588\"; expected_count \"5434.54\";\r\n6       Bayesembler     exon    20492633        20493290        .       +       .       gene_id \"graph_118857_plus\"; transcript_id \"graph_118857_plus_seq10\"; transcript_confidence \"1\"; FPK\r\nM \"6.17059\"; FPKM_sd \"0.36231\"; expected_count \"296.741\";\r\n\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/bioinformatics-centre/bayesembler/issues/comments/77579022","html_url":"https://github.com/bioinformatics-centre/bayesembler/issues/9#issuecomment-77579022","issue_url":"https://api.github.com/repos/bioinformatics-centre/bayesembler/issues/9","id":77579022,"user":{"login":"lassemaretty","id":5397865,"avatar_url":"https://avatars.githubusercontent.com/u/5397865?v=3","gravatar_id":"","url":"https://api.github.com/users/lassemaretty","html_url":"https://github.com/lassemaretty","followers_url":"https://api.github.com/users/lassemaretty/followers","following_url":"https://api.github.com/users/lassemaretty/following{/other_user}","gists_url":"https://api.github.com/users/lassemaretty/gists{/gist_id}","starred_url":"https://api.github.com/users/lassemaretty/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lassemaretty/subscriptions","organizations_url":"https://api.github.com/users/lassemaretty/orgs","repos_url":"https://api.github.com/users/lassemaretty/repos","events_url":"https://api.github.com/users/lassemaretty/events{/privacy}","received_events_url":"https://api.github.com/users/lassemaretty/received_events","type":"User","site_admin":false},"created_at":"2015-03-06T15:39:27Z","updated_at":"2015-03-06T15:39:27Z","body":"Thanks. We'll put a pre-release on GitHub as soon as we have it ready!\r\n\r\nBest, \r\n\r\nLasse"}}