<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); "><div style="font-family: Calibri, sans-serif; font-size: 14px; ">Yes. Perhaps this is the same issue Michael saw, although the one difference I see from his post is the Parent= attribute.</div><div style="font-family: Calibri, sans-serif; font-size: 14px; "><br></div><div style="font-family: Calibri, sans-serif; font-size: 14px; "><span class="Apple-style-span" style="font-family: Consolas; font-size: medium; ">--> </span><span class="Apple-style-span" style="font-family: Consolas; font-size: medium; ">Parent=augustus_masked-3-processed-gene-6.179-mRNA-1,augustus_masked-3-processed-gene-6.179-mRNA-1</span></div><div style="font-family: Calibri, sans-serif; font-size: 14px; "><span class="Apple-style-span" style="font-family: Consolas; font-size: medium; "><br></span></div><div style="font-family: Calibri, sans-serif; font-size: 14px; ">I have seen duplicate exons from GFF3 pass-through in the past, but if that's not being used I'<font class="Apple-style-span" face="Calibri,sans-serif">d be very appreciative of any test dataset you could give me.</font></div><div><font class="Apple-style-span" face="Calibri,sans-serif"><br></font></div><div><font class="Apple-style-span" face="Calibri,sans-serif">Thanks,</font></div><div><font class="Apple-style-span" face="Calibri,sans-serif">Carson</font></div><div><font class="Apple-style-span" face="Calibri,sans-serif"><br></font></div><div><font class="Apple-style-span" face="Calibri,sans-serif"><br></font></div><div><font class="Apple-style-span" face="Calibri,sans-serif"><br></font></div><div style="font-family: Calibri, sans-serif; font-size: 14px; "><br></div><span id="OLK_SRC_BODY_SECTION" style="font-size: 14px; font-family: Calibri, sans-serif; "><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> Daniel Hughes <<a href="mailto:dsth@ebi.ac.uk">dsth@ebi.ac.uk</a>><br><span style="font-weight:bold">Date: </span> Thursday, 16 May, 2013 12:38 PM<br><span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Cc: </span> Uma Maheswari <<a href="mailto:uma@ebi.ac.uk">uma@ebi.ac.uk</a>>, "<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> Re: [maker-devel] duplicate exons?<br></div><div><br></div><div dir="ltr"><div>hiya, are you using the same instance as michael at ebi as this sounds like the same problem he had last week and he wasn't running pass through. i've run 2.27 here 30+ times here and not seen this? is something very strange corrupted?<br><br></div>dan.<br></div><div class="gmail_extra"><br clear="all"><div>Daniel S. T. Hughes M.Biochem (Hons; Oxford), Ph.D (Cambridge)<br>-------------------------------------------------------------------------------------<br><a href="mailto:dsth@cantab.net">dsth@cantab.net</a><br><a href="mailto:dsth@cpan.org">dsth@cpan.org</a></div><br><br><div class="gmail_quote">2013/5/16 Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I think this also may be a result of using GFF3 pass-through. So if that<br>
is the case, could you send me any GFF3 files you gave maker in addition<br>
to the other files I asked for.<br><div class="im HOEnZb"><br>
Thanks,<br>
Carson<br><br><br><br>
On 13-05-16 12:08 PM, "Uma Maheswari" <<a href="mailto:uma@ebi.ac.uk">uma@ebi.ac.uk</a>> wrote:<br><br></div><div class="im HOEnZb">>Hi Carson,<br>
><br>
>When I was trying to load the Maker-2.27 results into ensembl, I found<br>
>that few hundreds of genes with 'duplicate exons' . When I looked in the<br>
>gff file, I found cases like this, where the exons are not actually<br>
>duplicated but have two Parents with same mRNA ID. This can be a<br>
>potential alternate transcript, attached to the same transcript by<br>
>mistake?<br>
><br>
>Many thanks<br>
>Uma<br>
><br>
><br>
><br>
><br>
><br>
>3 maker gene 524271 525467 . - .<br>
>ID=augustus_masked-3-processed-gene-6.179;Name=augustus_masked-3-processed<br>
>-gene-6.179<br>
>3 maker mRNA 524271 525467 . - .<br></div><div class="im HOEnZb">>ID=augustus_masked-3-processed-gene-6.179-mRNA-1;Parent=augustus_masked-3-<br>
>processed-gene-6.179;Name=augustus_masked-3-processed-gene-6.179-mRNA-1;_A<br></div><div class="HOEnZb"><div class="h5">>ED=0.50;_eAED=0.63;_QI=1476|0.33|0.75|1|0|0.25|4|0|406<br>
>3 maker exon 524271 524480 . - .<br>
>ID=augustus_masked-3-processed-gene-6.179-mRNA-1:exon:573;Parent=augustus_<br>
>masked-3-processed-gene-6.179-mRNA-1<br>
>3 maker exon 524538 525182 . - .<br>
>ID=augustus_masked-3-processed-gene-6.179-mRNA-1:exon:572;Parent=augustus_<br>
>masked-3-processed-gene-6.179-mRNA-1,augustus_masked-3-processed-gene-6.17<br>
>9-mRNA-1<br>
>3 maker exon 524271 525467 . - .<br>
>ID=augustus_masked-3-processed-gene-6.179-mRNA-1:exon:571;Parent=augustus_<br>
>masked-3-processed-gene-6.179-mRNA-1<br>
>3 maker CDS 524538 524903 . - 0<br>
>ID=augustus_masked-3-processed-gene-6.179-mRNA-1:cds;Parent=augustus_maske<br>
>d-3-processed-gene-6.179-mRNA-1<br>
>3 maker CDS 524538 525182 . - 0<br>
>ID=augustus_masked-3-processed-gene-6.179-mRNA-1:cds;Parent=augustus_maske<br>
>d-3-processed-gene-6.179-mRNA-1<br>
>3 maker CDS 524271 524480 . - 0<br>
>ID=augustus_masked-3-processed-gene-6.179-mRNA-1:cds;Parent=augustus_maske<br>
>d-3-processed-gene-6.179-mRNA-1<br>
>3 maker five_prime_UTR 524271 525467 . - .<br>
>ID=augustus_masked-3-processed-gene-6.179-mRNA-1:five_prime_utr;Parent=aug<br>
>ustus_masked-3-processed-gene-6.179-mRNA-1<br>
>3 maker five_prime_UTR 524904 525182 . - .<br>
>ID=augustus_masked-3-processed-gene-6.179-mRNA-1:five_prime_utr;Parent=aug<br>
>ustus_masked-3-processed-gene-6.179-mRNA-1<br>
><br>
><br>
>_______________________________________________<br>
>maker-devel mailing list<br>
><a href="mailto:maker-devel@box290.bluehost.com">maker-devel@box290.bluehost.com</a><br>
><a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org" target="_blank">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a><br><br><br><br>
_______________________________________________<br>
maker-devel mailing list<br><a href="mailto:maker-devel@box290.bluehost.com">maker-devel@box290.bluehost.com</a><br><a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org" target="_blank">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a><br><br></div></div></blockquote></div><br></div></span></body></html>