<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Jacques<div class=""><br class=""></div><div class="">Thanks for your input. We’re currently reworking our own parsers and exporters for all the common formats, including GFF3, so we’ll take your comments into consideration.</div><div class=""><br class=""></div><div class="">Cheers</div><div class=""><br class=""></div><div class="">Anne</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On 31 Oct 2016, at 10:01, Jacques Dainat <<a href="mailto:jacques.dainat@bils.se" class="">jacques.dainat@bils.se</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html charset=utf-8" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class="">Hi,</div><div class=""><br class=""></div><div class="">Dear all,</div><div class=""><br class=""></div><div class="">I'm working in an annotation service and we use the gff3 format as a central format for everything we are doing. So, we have scripts to check the gff3 and correct them if needed.</div><div class="">When I was working with the gff3 file Homo_sapiens.GRCh37.82.gff3 coming from your work, some peculiarities that I have never seen before popped up.</div><div class=""><br class=""></div><div class="">First of all I would like to explain quickly how we parse our data:</div><div class=""><br class=""></div><div class="">We usually parse our data paying strong attention about the “<b class="">type</b>” (3rd column) and sorting them in 3 levels structure:</div><div class="">Level1 => Features that do not have <b class="">Parent:</b> gene, pseudogene, lincrna_gene, mirna_gene etc.</div><div class="">Level2 => Features that have <b class="">Parent</b> and <b class="">Children:</b> mrna, trna, snorna, transcript, processed_pseudogene, etc.</div><div class="">Level3 => Features that have <b class="">Parent</b> but <b class="">no Children:</b> cds, exon, utr, tts, stop_codon,sig_peptide, etc.</div><div class=""><br class=""></div><div class="">This works quite fine with gff3 coming from many different sources, but when coming to parse your data it doesn’t work properly.</div><div class="">Indeed there is some inconsistency within the 3rd column and we cannot either use the biotype attribute of the 9th column that seems to vary within a same feature.</div><div class="">I would like to know if you can make an effort to homogenise those things for future data releases.</div><div class=""><br class=""></div><div class="">In order to better explain the thing, and argument it, here is some examples:</div><div class="">========================================================</div><div class=""><br class=""></div><div class="">************************************************</div><div class=""><b class=""> <u class="">FIRST</u></b>, examples where things are fine:</div><div class="">************************************************</div><div class=""><div class=""><div class="">###</div></div></div><div class=""><div class=""><div class="">1<span class="Apple-tab-span" style="white-space: pre;"> </span>ensembl<span class="Apple-tab-span" style="white-space: pre;"> </span>snRNA_gene<span class="Apple-tab-span" style="white-space: pre;"> </span>13384735<span class="Apple-tab-span" style="white-space: pre;"> </span>13384841<span class="Apple-tab-span" style="white-space: pre;"> </span>.<span class="Apple-tab-span" style="white-space: pre;"> </span>-<span class="Apple-tab-span" style="white-space: pre;"> </span>.<span class="Apple-tab-span" style="white-space: pre;"> </span>ID=gene:ENSG00000207511;Name=RNU6-771P;biotype=snRNA;description=RNA%2C U6 small nuclear 771%2C pseudogene [Source:HGNC Symbol%3BAcc:47734];gene_id=ENSG00000207511;logic_name=ncrna;version=1</div><div class="">1<span class="Apple-tab-span" style="white-space: pre;"> </span>ensembl<span class="Apple-tab-span" style="white-space: pre;"> </span>snRNA<span class="Apple-tab-span" style="white-space: pre;"> </span>13384735<span class="Apple-tab-span" style="white-space: pre;"> </span>13384841<span class="Apple-tab-span" style="white-space: pre;"> </span>.<span class="Apple-tab-span" style="white-space: pre;"> </span>-<span class="Apple-tab-span" style="white-space: pre;"> </span>.<span class="Apple-tab-span" style="white-space: pre;"> </span>ID=transcript:ENST00000384780;Parent=gene:ENSG00000207511;Name=RNU6-771P-201;biotype=snRNA;tag=basic;transcript_id=ENST00000384780;version=1</div><div class="">1<span class="Apple-tab-span" style="white-space: pre;"> </span>ensembl<span class="Apple-tab-span" style="white-space: pre;"> </span>exon<span class="Apple-tab-span" style="white-space: pre;"> </span>13384735<span class="Apple-tab-span" style="white-space: pre;"> </span>13384841<span class="Apple-tab-span" style="white-space: pre;"> </span>.<span class="Apple-tab-span" style="white-space: pre;"> </span>-<span class="Apple-tab-span" style="white-space: pre;"> </span>.<span class="Apple-tab-span" style="white-space: pre;"> </span>Parent=transcript:ENST00000384780;Name=ENSE00001807562;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=ENSE00001807562;rank=1;version=1</div><div class="">###</div></div><div class=""><div class="">OK:<span class="Apple-tab-span" style="white-space:pre"> </span>Based on 3rd column: snRNA_gene <= snRNA <= exon</div><div class="">OK:<span class="Apple-tab-span" style="white-space:pre"> </span>biotype attribute: <span class="Apple-tab-span" style="white-space:pre"> </span> snRNA <= snRNA</div></div><div class=""><br class=""></div><div class=""><div class="">###</div><div class="">1<span class="Apple-tab-span" style="white-space: pre;"> </span>havana<span class="Apple-tab-span" style="white-space: pre;"> </span>lincRNA_gene<span class="Apple-tab-span" style="white-space: pre;"> </span>32814795<span class="Apple-tab-span" style="white-space: pre;"> </span>32816264<span class="Apple-tab-span" style="white-space: pre;"> </span>.<span class="Apple-tab-span" style="white-space: pre;"> </span>-<span class="Apple-tab-span" style="white-space: pre;"> </span>.<span class="Apple-tab-span" style="white-space: pre;"> </span>ID=gene:ENSG00000233775;Name=RP4-811H24.9;biotype=lincRNA;gene_id=ENSG00000233775;logic_name=havana;version=1</div><div class="">1<span class="Apple-tab-span" style="white-space: pre;"> </span>havana<span class="Apple-tab-span" style="white-space: pre;"> </span>lincRNA<span class="Apple-tab-span" style="white-space: pre;"> </span>32814795<span class="Apple-tab-span" style="white-space: pre;"> </span>32816264<span class="Apple-tab-span" style="white-space: pre;"> </span>.<span class="Apple-tab-span" style="white-space: pre;"> </span>-<span class="Apple-tab-span" style="white-space: pre;"> </span>.<span class="Apple-tab-span" style="white-space: pre;"> </span>ID=transcript:ENST00000448134;Parent=gene:ENSG00000233775;Name=RP4-811H24.9-001;biotype=lincRNA;havana_transcript=OTTHUMT00000020212;havana_version=3;tag=basic;transcript_id=ENST00000448134;version=1</div><div class="">1<span class="Apple-tab-span" style="white-space: pre;"> </span>havana<span class="Apple-tab-span" style="white-space: pre;"> </span>exon<span class="Apple-tab-span" style="white-space: pre;"> </span>32814795<span class="Apple-tab-span" style="white-space: pre;"> </span>32815422<span class="Apple-tab-span" style="white-space: pre;"> </span>.<span class="Apple-tab-span" style="white-space: pre;"> </span>-<span class="Apple-tab-span" style="white-space: pre;"> </span>.<span class="Apple-tab-span" style="white-space: pre;"> </span>Parent=transcript:ENST00000448134;Name=ENSE00001776478;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=ENSE00001776478;rank=2;version=1</div><div class="">1<span class="Apple-tab-span" style="white-space: pre;"> </span>havana<span class="Apple-tab-span" style="white-space: pre;"> </span>exon<span class="Apple-tab-span" style="white-space: pre;"> </span>32816206<span class="Apple-tab-span" style="white-space: pre;"> </span>32816264<span class="Apple-tab-span" style="white-space: pre;"> </span>.<span class="Apple-tab-span" style="white-space: pre;"> </span>-<span class="Apple-tab-span" style="white-space: pre;"> </span>.<span class="Apple-tab-span" style="white-space: pre;"> </span>Parent=transcript:ENST00000448134;Name=ENSE00001624254;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=ENSE00001624254;rank=1;version=1</div><div class="">###</div></div><div class=""><div class="">OK:<span class="Apple-tab-span" style="white-space:pre"> </span>Based on 3rd column: lincRNA_gene <= lincRNA <= exon</div><div class="">OK:<span class="Apple-tab-span" style="white-space:pre"> </span>biotype attribute: <span class="Apple-tab-span" style="white-space:pre"> </span> lincRNA <= lincRNA</div></div><div class=""><br class=""></div><div class=""><div class="">###</div><div class="">1<span class="Apple-tab-span" style="white-space: pre;"> </span>ensembl_havana<span class="Apple-tab-span" style="white-space: pre;"> </span>gene<span class="Apple-tab-span" style="white-space: pre;"> </span>13474689<span class="Apple-tab-span" style="white-space: pre;"> </span>13477522<span class="Apple-tab-span" style="white-space: pre;"> </span>.<span class="Apple-tab-span" style="white-space: pre;"> </span>-<span class="Apple-tab-span" style="white-space: pre;"> </span>.<span class="Apple-tab-span" style="white-space: pre;"> </span>ID=gene:ENSG00000204491;Name=PRAMEF18;biotype=protein_coding;description=PRAME family member 18 [Source:HGNC Symbol%3BAcc:30693];gene_id=ENSG00000204491;logic_name=ensembl_havana_gene;version=2</div><div class="">1<span class="Apple-tab-span" style="white-space: pre;"> </span>ensembl_havana<span class="Apple-tab-span" style="white-space: pre;"> </span>transcript<span class="Apple-tab-span" style="white-space: pre;"> </span>13474689<span class="Apple-tab-span" style="white-space: pre;"> </span>13477522<span class="Apple-tab-span" style="white-space: pre;"> </span>.<span class="Apple-tab-span" style="white-space: pre;"> </span>-<span class="Apple-tab-span" style="white-space: pre;"> </span>.<span class="Apple-tab-span" style="white-space: pre;"> </span>ID=transcript:ENST00000376126;Parent=gene:ENSG00000204491;Name=PRAMEF18-001;biotype=protein_coding;ccdsid=CCDS41258.1;havana_transcript=OTTHUMT00000008177;havana_version=2;tag=basic;transcript_id=ENST00000376126;version=2</div><div class="">1<span class="Apple-tab-span" style="white-space: pre;"> </span>ensembl_havana<span class="Apple-tab-span" style="white-space: pre;"> </span>exon<span class="Apple-tab-span" style="white-space: pre;"> </span>13474689<span class="Apple-tab-span" style="white-space: pre;"> </span>13475262<span class="Apple-tab-span" style="white-space: pre;"> </span>.<span class="Apple-tab-span" style="white-space: pre;"> </span>-<span class="Apple-tab-span" style="white-space: pre;"> </span>.<span class="Apple-tab-span" style="white-space: pre;"> </span>Parent=transcript:ENST00000376126;Name=ENSE00001592884;constitutive=1;ensembl_end_phase=-1;ensembl_phase=2;exon_id=ENSE00001592884;rank=3;version=2</div><div class="">1<span class="Apple-tab-span" style="white-space: pre;"> </span>ensembl_havana<span class="Apple-tab-span" style="white-space: pre;"> </span>CDS<span class="Apple-tab-span" style="white-space: pre;"> </span>13474689<span class="Apple-tab-span" style="white-space: pre;"> </span>13475262<span class="Apple-tab-span" style="white-space: pre;"> </span>.<span class="Apple-tab-span" style="white-space: pre;"> </span>-<span class="Apple-tab-span" style="white-space: pre;"> </span>1<span class="Apple-tab-span" style="white-space: pre;"> </span>ID=CDS:ENSP00000365294;Parent=transcript:ENST00000376126;protein_id=ENSP00000365294</div><div class="">1<span class="Apple-tab-span" style="white-space: pre;"> </span>ensembl_havana<span class="Apple-tab-span" style="white-space: pre;"> </span>exon<span class="Apple-tab-span" style="white-space: pre;"> </span>13476271<span class="Apple-tab-span" style="white-space: pre;"> </span>13476849<span class="Apple-tab-span" style="white-space: pre;"> </span>.<span class="Apple-tab-span" style="white-space: pre;"> </span>-<span class="Apple-tab-span" style="white-space: pre;"> </span>.<span class="Apple-tab-span" style="white-space: pre;"> </span>Parent=transcript:ENST00000376126;Name=ENSE00001620306;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=ENSE00001620306;rank=2;version=1</div><div class="">1<span class="Apple-tab-span" style="white-space: pre;"> </span>ensembl_havana<span class="Apple-tab-span" style="white-space: pre;"> </span>CDS<span class="Apple-tab-span" style="white-space: pre;"> </span>13476271<span class="Apple-tab-span" style="white-space: pre;"> </span>13476849<span class="Apple-tab-span" style="white-space: pre;"> </span>.<span class="Apple-tab-span" style="white-space: pre;"> </span>-<span class="Apple-tab-span" style="white-space: pre;"> </span>1<span class="Apple-tab-span" style="white-space: pre;"> </span>ID=CDS:ENSP00000365294;Parent=transcript:ENST00000376126;protein_id=ENSP00000365294</div><div class="">1<span class="Apple-tab-span" style="white-space: pre;"> </span>ensembl_havana<span class="Apple-tab-span" style="white-space: pre;"> </span>exon<span class="Apple-tab-span" style="white-space: pre;"> </span>13477236<span class="Apple-tab-span" style="white-space: pre;"> </span>13477522<span class="Apple-tab-span" style="white-space: pre;"> </span>.<span class="Apple-tab-span" style="white-space: pre;"> </span>-<span class="Apple-tab-span" style="white-space: pre;"> </span>.<span class="Apple-tab-span" style="white-space: pre;"> </span>Parent=transcript:ENST00000376126;Name=ENSE00003445415;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=ENSE00003445415;rank=1;version=1</div><div class="">1<span class="Apple-tab-span" style="white-space: pre;"> </span>ensembl_havana<span class="Apple-tab-span" style="white-space: pre;"> </span>CDS<span class="Apple-tab-span" style="white-space: pre;"> </span>13477236<span class="Apple-tab-span" style="white-space: pre;"> </span>13477522<span class="Apple-tab-span" style="white-space: pre;"> </span>.<span class="Apple-tab-span" style="white-space: pre;"> </span>-<span class="Apple-tab-span" style="white-space: pre;"> </span>0<span class="Apple-tab-span" style="white-space: pre;"> </span>ID=CDS:ENSP00000365294;Parent=transcript:ENST00000376126;protein_id=ENSP00000365294</div><div class="">###</div></div></div><div class=""><div class="">OK:<span class="Apple-tab-span" style="white-space:pre"> </span>Based on 3rd column: gene <= transcript <= exon,CDS</div><div class="">OK:<span class="Apple-tab-span" style="white-space:pre"> </span>biotype attribute: protein_coding <= protein_coding</div></div><div class=""><br class=""></div><div class=""><div class="">************************************************</div><div class=""><b class=""> <u class="">SECOND</u></b>, 3rd column OK but biotype changes:</div><div class="">************************************************</div></div><div class=""><div class=""><br class=""></div><div class=""><div class="">###</div><div class="">10<span class="Apple-tab-span" style="white-space: pre;"> </span>ensembl_havana<span class="Apple-tab-span" style="white-space: pre;"> </span>pseudogene<span class="Apple-tab-span" style="white-space: pre;"> </span>112696380<span class="Apple-tab-span" style="white-space: pre;"> </span>112696991<span class="Apple-tab-span" style="white-space: pre;"> </span>.<span class="Apple-tab-span" style="white-space: pre;"> </span>-<span class="Apple-tab-span" style="white-space: pre;"> </span>.<span class="Apple-tab-span" style="white-space: pre;"> </span>ID=gene:ENSG00000234118;Name=RPL13AP6;biotype=pseudogene;description=ribosomal protein L13a pseudogene 6 [Source:HGNC Symbol%3BAcc:23737];gene_id=ENSG00000234118;logic_name=ensembl_havana_gene;version=1</div><div class="">10<span class="Apple-tab-span" style="white-space: pre;"> </span>ensembl_havana<span class="Apple-tab-span" style="white-space: pre;"> </span>processed_pseudogene<span class="Apple-tab-span" style="white-space: pre;"> </span>112696380<span class="Apple-tab-span" style="white-space: pre;"> </span>112696991<span class="Apple-tab-span" style="white-space: pre;"> </span>.<span class="Apple-tab-span" style="white-space: pre;"> </span>-<span class="Apple-tab-span" style="white-space: pre;"> </span>.<span class="Apple-tab-span" style="white-space: pre;"> </span>ID=transcript:ENST00000430133;Parent=gene:ENSG00000234118;Name=RPL13AP6-001;biotype=processed_pseudogene;havana_transcript=OTTHUMT00000050371;havana_version=1;tag=basic;transcript_id=ENST00000430133;version=1</div><div class="">10<span class="Apple-tab-span" style="white-space: pre;"> </span>ensembl_havana<span class="Apple-tab-span" style="white-space: pre;"> </span>exon<span class="Apple-tab-span" style="white-space: pre;"> </span>112696380<span class="Apple-tab-span" style="white-space: pre;"> </span>112696991<span class="Apple-tab-span" style="white-space: pre;"> </span>.<span class="Apple-tab-span" style="white-space: pre;"> </span>-<span class="Apple-tab-span" style="white-space: pre;"> </span>.<span class="Apple-tab-span" style="white-space: pre;"> </span>Parent=transcript:ENST00000430133;Name=ENSE00002511651;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=ENSE00002511651;rank=1;version=1</div><div class="">###</div></div><div class=""></div></div><div class=""><div class=""><div class="">OK:<span class="Apple-tab-span" style="white-space:pre"> </span>Based on 3rd column : pseudogene <= processed_pseudogene <= exon</div><div class=""><b class="">??:<span class="Apple-tab-span" style="white-space:pre"> </span></b>biotype attribute : <span class="Apple-tab-span" style="white-space:pre"> </span> pseudogene <= processed_pseudogene</div></div></div><div class=""><br class=""></div><div class=""><b class="">Question1 :</b> Why the biotype change ? Will not be more coherent to have the processed_pseudogene biotype for the pseudogene feature too ?</div><div class=""><br class=""></div><div class=""><div class="">************************************************</div><div class=""><b class=""> <u class="">THIRD</u></b>, 3rd column does not change but biotype changes:</div><div class="">************************************************</div></div><div class=""><br class=""></div><div class=""><div class="">###</div><div class="">1<span class="Apple-tab-span" style="white-space:pre"> </span>havana<span class="Apple-tab-span" style="white-space:pre"> </span>pseudogene<span class="Apple-tab-span" style="white-space:pre"> </span>176241619<span class="Apple-tab-span" style="white-space:pre"> </span>176242538<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>+<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>ID=gene:ENSG00000227815;Name=RP11-195C7.3;biotype=pseudogene;gene_id=ENSG00000227815;logic_name=havana;version=2</div><div class="">1<span class="Apple-tab-span" style="white-space:pre"> </span>havana<span class="Apple-tab-span" style="white-space:pre"> </span>pseudogene<span class="Apple-tab-span" style="white-space:pre"> </span>176241619<span class="Apple-tab-span" style="white-space:pre"> </span>176242538<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>+<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>ID=transcript:ENST00000440296;Parent=gene:ENSG00000227815;Name=RP11-195C7.3-001;biotype=unprocessed_pseudogene;havana_transcript=OTTHUMT00000084685;havana_version=2;tag=basic;transcript_id=ENST00000440296;version=2</div><div class="">1<span class="Apple-tab-span" style="white-space:pre"> </span>havana<span class="Apple-tab-span" style="white-space:pre"> </span>exon<span class="Apple-tab-span" style="white-space:pre"> </span>176241619<span class="Apple-tab-span" style="white-space:pre"> </span>176241675<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>+<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>Parent=transcript:ENST00000440296;Name=ENSE00001660785;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=ENSE00001660785;rank=1;version=2</div><div class="">1<span class="Apple-tab-span" style="white-space:pre"> </span>havana<span class="Apple-tab-span" style="white-space:pre"> </span>exon<span class="Apple-tab-span" style="white-space:pre"> </span>176241743<span class="Apple-tab-span" style="white-space:pre"> </span>176242168<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>+<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>Parent=transcript:ENST00000440296;Name=ENSE00001739151;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=ENSE00001739151;rank=2;version=2</div><div class="">1<span class="Apple-tab-span" style="white-space:pre"> </span>havana<span class="Apple-tab-span" style="white-space:pre"> </span>exon<span class="Apple-tab-span" style="white-space:pre"> </span>176242227<span class="Apple-tab-span" style="white-space:pre"> </span>176242538<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>+<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>Parent=transcript:ENST00000440296;Name=ENSE00001773509;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=ENSE00001773509;rank=3;version=2</div><div class="">###</div></div><div class=""><div class=""><b class="">??:<span class="Apple-tab-span" style="white-space:pre"> </span></b>Based on 3rd column : <b class="">pseudogene <= pseudogene</b> <= exon</div><div class=""><b class="">??:<span class="Apple-tab-span" style="white-space:pre"> </span></b>biotype attribute :<span class="Apple-tab-span" style="white-space:pre"> </span> pseudogene <= unprocessed_pseudogene</div></div><div class=""><br class=""></div><div class=""><b class="">Question2 :</b> Why the second feature is also a pseudogene ? Will not be more coherent to have a sort of subclass of pseudogene like unprocessed_pseudogene as you do for the biotype in that case ?</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span> As for the question1, why the biotype change ? Will not be better to have unprocessed_pseudogene for the top feature too ?</div><div class=""><br class=""></div><div class=""><div class="">###</div><div class="">1<span class="Apple-tab-span" style="white-space:pre"> </span>havana<span class="Apple-tab-span" style="white-space:pre"> </span>pseudogene<span class="Apple-tab-span" style="white-space:pre"> </span>13411551<span class="Apple-tab-span" style="white-space:pre"> </span>13414482<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>+<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>ID=gene:ENSG00000237700;Name=RP11-219C24.6;biotype=pseudogene;gene_id=ENSG00000237700;logic_name=havana;version=1</div><div class="">1<span class="Apple-tab-span" style="white-space:pre"> </span>havana<span class="Apple-tab-span" style="white-space:pre"> </span>pseudogene<span class="Apple-tab-span" style="white-space:pre"> </span>13411551<span class="Apple-tab-span" style="white-space:pre"> </span>13414482<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>+<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>ID=transcript:ENST00000437300;Parent=gene:ENSG00000237700;Name=RP11-219C24.6-001;biotype=unitary_pseudogene;havana_transcript=OTTHUMT00000022042;havana_version=1;tag=basic;transcript_id=ENST00000437300;version=1</div><div class="">1<span class="Apple-tab-span" style="white-space:pre"> </span>havana<span class="Apple-tab-span" style="white-space:pre"> </span>exon<span class="Apple-tab-span" style="white-space:pre"> </span>13411551<span class="Apple-tab-span" style="white-space:pre"> </span>13411837<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>+<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>Parent=transcript:ENST00000437300;Name=ENSE00001677077;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=ENSE00001677077;rank=1;version=1</div><div class="">1<span class="Apple-tab-span" style="white-space:pre"> </span>havana<span class="Apple-tab-span" style="white-space:pre"> </span>exon<span class="Apple-tab-span" style="white-space:pre"> </span>13412234<span class="Apple-tab-span" style="white-space:pre"> </span>13412812<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>+<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>Parent=transcript:ENST00000437300;Name=ENSE00001715540;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=ENSE00001715540;rank=2;version=1</div><div class="">1<span class="Apple-tab-span" style="white-space:pre"> </span>havana<span class="Apple-tab-span" style="white-space:pre"> </span>exon<span class="Apple-tab-span" style="white-space:pre"> </span>13413924<span class="Apple-tab-span" style="white-space:pre"> </span>13414482<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>+<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>Parent=transcript:ENST00000437300;Name=ENSE00001784031;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=ENSE00001784031;rank=3;version=1</div><div class="">###</div></div><div class=""><div class=""><b class="">??:<span class="Apple-tab-span" style="white-space:pre"> </span></b>Based on 3rd column : <b class="">pseudogene <= pseudogene</b> <= exon</div><div class=""><b class="">??:<span class="Apple-tab-span" style="white-space:pre"> </span></b>biotype attribute : pseudogene <= unitary_pseudogene</div></div><div class=""><br class=""></div><div class="">The same as question2 ...</div><div class=""><br class=""></div><div class=""><div class="">*************************************************</div><div class=""><b class=""> <u class="">FOURTH</u></b>, same feature used differently :</div><div class="">*************************************************</div></div><div class=""><br class=""></div><div class=""><div class="">### Locus1</div><div class="">1<span class="Apple-tab-span" style="white-space:pre"> </span>havana<span class="Apple-tab-span" style="white-space:pre"> </span>processed_transcript<span class="Apple-tab-span" style="white-space:pre"> </span>141474<span class="Apple-tab-span" style="white-space:pre"> </span>173862<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>-<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>ID=gene:ENSG00000241860;Name=RP11-34P13.13;biotype=processed_transcript;gene_id=ENSG00000241860;logic_name=havana;version=2</div><div class="">1<span class="Apple-tab-span" style="white-space:pre"> </span>havana<span class="Apple-tab-span" style="white-space:pre"> </span>transcript<span class="Apple-tab-span" style="white-space:pre"> </span>141474<span class="Apple-tab-span" style="white-space:pre"> </span>149707<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>-<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>ID=transcript:ENST00000484859;Parent=gene:ENSG00000241860;Name=RP11-34P13.13-004;biotype=antisense;havana_transcript=OTTHUMT00000007035;havana_version=1;tag=basic;transcript_id=ENST00000484859;version=1</div><div class="">1<span class="Apple-tab-span" style="white-space:pre"> </span>havana<span class="Apple-tab-span" style="white-space:pre"> </span>exon<span class="Apple-tab-span" style="white-space:pre"> </span>141474<span class="Apple-tab-span" style="white-space:pre"> </span>143011<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>-<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>Parent=transcript:ENST00000484859;Name=ENSE00001911218;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=ENSE00001911218;rank=2;version=1</div><div class="">1<span class="Apple-tab-span" style="white-space:pre"> </span>havana<span class="Apple-tab-span" style="white-space:pre"> </span>exon<span class="Apple-tab-span" style="white-space:pre"> </span>146386<span class="Apple-tab-span" style="white-space:pre"> </span>149707<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>-<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>Parent=transcript:ENST00000484859;Name=ENSE00001860404;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=ENSE00001860404;rank=1;version=1</div></div><div class=""><div class="">### Locus2</div></div><div class=""><div class="">1<span class="Apple-tab-span" style="white-space:pre"> </span>ensembl_havana<span class="Apple-tab-span" style="white-space:pre"> </span>pseudogene<span class="Apple-tab-span" style="white-space:pre"> </span>11869<span class="Apple-tab-span" style="white-space:pre"> </span>14412<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>+<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>ID=gene:ENSG00000223972;Name=DDX11L1;biotype=pseudogene;description=DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11 like 1 [Source:HGNC Symbol%3BAcc:37102];gene_id=ENSG00000223972;logic_name=ensembl_havana_gene;version=4</div><div class="">1<span class="Apple-tab-span" style="white-space:pre"> </span>ensembl_havana<span class="Apple-tab-span" style="white-space:pre"> </span>processed_transcript<span class="Apple-tab-span" style="white-space:pre"> </span>11869<span class="Apple-tab-span" style="white-space:pre"> </span>14409<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>+<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>ID=transcript:ENST00000456328;Parent=gene:ENSG00000223972;Name=DDX11L1-002;biotype=processed_transcript;havana_transcript=OTTHUMT00000362751;havana_version=1;tag=basic;transcript_id=ENST00000456328;version=2</div><div class="">1<span class="Apple-tab-span" style="white-space:pre"> </span>havana<span class="Apple-tab-span" style="white-space:pre"> </span>exon<span class="Apple-tab-span" style="white-space:pre"> </span>11869<span class="Apple-tab-span" style="white-space:pre"> </span>12227<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>+<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>Parent=transcript:ENST00000456328;Name=ENSE00002234944;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=ENSE00002234944;rank=1;version=1</div><div class="">1<span class="Apple-tab-span" style="white-space:pre"> </span>havana<span class="Apple-tab-span" style="white-space:pre"> </span>exon<span class="Apple-tab-span" style="white-space:pre"> </span>12613<span class="Apple-tab-span" style="white-space:pre"> </span>12721<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>+<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>Parent=transcript:ENST00000456328;Name=ENSE00003582793;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=ENSE00003582793;rank=2;version=1</div><div class="">1<span class="Apple-tab-span" style="white-space:pre"> </span>havana<span class="Apple-tab-span" style="white-space:pre"> </span>exon<span class="Apple-tab-span" style="white-space:pre"> </span>13221<span class="Apple-tab-span" style="white-space:pre"> </span>14409<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>+<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>Parent=transcript:ENST00000456328;Name=ENSE00002312635;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=ENSE00002312635;rank=3;version=1</div></div><div class="">###</div><div class=""><div class=""><b class="">??</b> => For the first locus the processed_transcript is a <b class="">top level</b> feature (has a transcript child), then for the second locus the processed_transcript is a child of the pseudogene feature.</div></div><div class=""><b class=""><br class=""></b></div><div class=""><b class="">Question3: </b>Why a same feature (processed_transcript) does not follow the same schema ? In my sense, it must be always either a <b class="">top level </b>feature or a child of a top level feature.</div><div class=""><br class=""></div><div class=""><div class="">********************************</div><div class=""><b class=""> <u class="">FIFTH</u></b>, semantic choice :</div><div class="">********************************</div></div><div class=""><br class=""></div><div class=""><div class="">###</div><div class="">1<span class="Apple-tab-span" style="white-space:pre"> </span>ensembl<span class="Apple-tab-span" style="white-space:pre"> </span>RNA<span class="Apple-tab-span" style="white-space:pre"> </span>1340841<span class="Apple-tab-span" style="white-space:pre"> </span>1341132<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>-<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>ID=gene:ENSG00000264293;Name=RN7SL657P;biotype=misc_RNA;description=RNA%2C 7SL%2C cytoplasmic 657%2C pseudogene [Source:HGNC Symbol%3BAcc:46673];gene_id=ENSG00000264293;logic_name=ncrna;version=1</div><div class="">1<span class="Apple-tab-span" style="white-space:pre"> </span>ensembl<span class="Apple-tab-span" style="white-space:pre"> </span>transcript<span class="Apple-tab-span" style="white-space:pre"> </span>1340841<span class="Apple-tab-span" style="white-space:pre"> </span>1341132<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>-<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>ID=transcript:ENST00000582431;Parent=gene:ENSG00000264293;Name=RN7SL657P-201;biotype=misc_RNA;tag=basic;transcript_id=ENST00000582431;version=1</div><div class="">1<span class="Apple-tab-span" style="white-space:pre"> </span>ensembl<span class="Apple-tab-span" style="white-space:pre"> </span>exon<span class="Apple-tab-span" style="white-space:pre"> </span>1340841<span class="Apple-tab-span" style="white-space:pre"> </span>1341132<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>-<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>Parent=transcript:ENST00000582431;Name=ENSE00002720632;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=ENSE00002720632;rank=1;version=1</div><div class="">###</div></div><div class="">??: Just a semantic choice but a RNA that has a transcript has child is a bit strange. </div><div class=""><br class=""></div><div class=""><b class="">Remark:</b> Change the transcript by RNA and have has top level feature something like RNA<b class="">_gene </b>as you do for all other RNA feature types would be great.</div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">So I would like some clarifications about the choices you did when creating your gff3 annotation file. I would like to know as well if it’s possible for you to make the thing more consistent, it would be easier for everybody I guess.</div><div class="">Thanks in advance,</div><div class=""><br class=""></div><div class=""><div class="">Best regards,</div></div><div class=""><br class=""></div><div apple-content-edited="true" class="">
<div style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-ligatures: normal; font-variant-position: normal; font-variant-caps: normal; font-variant-numeric: normal; font-variant-alternates: normal; font-variant-east-asian: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-ligatures: normal; font-variant-position: normal; font-variant-caps: normal; font-variant-numeric: normal; font-variant-alternates: normal; font-variant-east-asian: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class="">Jacques Dainat, PhD</div><div class="">NBIS (National Bioinformatics Infrastructure Sweden)</div><div class="">Genome Annotation Service</div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><br class=""></div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><u class="">Address:</u><span class="Apple-converted-space"> </span>(room E10:4204 - last floor)</div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Uppsala University, BMC<br class="">Department of Medical Biochemistry Microbiology, Genomics</div>Husargatan 3, box 582</div><div style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-ligatures: normal; font-variant-position: normal; font-variant-caps: normal; font-variant-numeric: normal; font-variant-alternates: normal; font-variant-east-asian: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">S-75123 Uppsala Sweden</div><div style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-ligatures: normal; font-variant-position: normal; font-variant-caps: normal; font-variant-numeric: normal; font-variant-alternates: normal; font-variant-east-asian: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Phone: 01 84 71 46 25</div></div></div></div></div></div></div></div></div></div>_______________________________________________<br class="">Dev mailing list <a href="mailto:Dev@ensembl.org" class="">Dev@ensembl.org</a><br class="">Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" class="">http://lists.ensembl.org/mailman/listinfo/dev</a><br class="">Ensembl Blog: <a href="http://www.ensembl.info/" class="">http://www.ensembl.info/</a><br class=""></div></blockquote></div><br class=""></div></body></html>