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Hi Carson,<br>
<br>
I checked with Michael, this is different from what he saw, he had
entire segements of gff files duplicated, In this case, just Parent
id is. <br>
I am preparing the files you asked for, will send them soon<br>
<br>
thanks<br>
Uma<br>
<br>
<br>
On 16/05/13 17:50, Carson Holt wrote:
<blockquote cite="mid:CDBA846A.1DFFA%25carsonhh@gmail.com"
type="cite">
<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-width: 1pt medium medium;
border-style: solid none none; border-color: rgb(181, 196,
223) -moz-use-text-color -moz-use-text-color; padding: 3pt 0in
0in;"><span style="font-weight: bold;">From: </span> Daniel
Hughes <<a moz-do-not-send="true"
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
moz-do-not-send="true" href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><br>
<span style="font-weight: bold;">Cc: </span> Uma Maheswari
<<a moz-do-not-send="true" href="mailto:uma@ebi.ac.uk">uma@ebi.ac.uk</a>>,
"<a moz-do-not-send="true"
href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>"
<<a moz-do-not-send="true"
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 moz-do-not-send="true" href="mailto:dsth@cantab.net">dsth@cantab.net</a><br>
<a moz-do-not-send="true" 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 moz-do-not-send="true"
href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span><br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
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
moz-do-not-send="true" 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>
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</blockquote>
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</span></blockquote>
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