Dear Carson,<div><br></div><div>The new version does indeed fix the problem!</div><div><br></div><div>However, I noticed that some of the CDS annotations were swallowed. This seems to affect a ~600 genes.</div><div><br></div>
<div>e.g. input:</div><div><br></div><div><div>pbar_scf7180000349951<span class="Apple-tab-span" style="white-space:pre"> </span>maker<span class="Apple-tab-span" style="white-space:pre"> </span>mRNA<span class="Apple-tab-span" style="white-space:pre"> </span>98033<span class="Apple-tab-span" style="white-space:pre"> </span>98530<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=PB12301-RA;Parent=PB12301;Name=PB12301-RA;Alias=maker-pbar_scf7180000349951-snap-gene-1.17-mRNA-1;_AED=1.00;_QI=0|0|0|0|0|0|2|0|81;</div>
<div>pbar_scf7180000349951<span class="Apple-tab-span" style="white-space:pre"> </span>maker<span class="Apple-tab-span" style="white-space:pre"> </span>exon<span class="Apple-tab-span" style="white-space:pre"> </span>98393<span class="Apple-tab-span" style="white-space:pre"> </span>98530<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=PB12301-RA:exon:10283;Parent=PB12301-RA;</div>
<div>pbar_scf7180000349951<span class="Apple-tab-span" style="white-space:pre"> </span>maker<span class="Apple-tab-span" style="white-space:pre"> </span>exon<span class="Apple-tab-span" style="white-space:pre"> </span>98033<span class="Apple-tab-span" style="white-space:pre"> </span>98140<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=PB12301-RA:exon:10284;Parent=PB12301-RA;</div>
<div>pbar_scf7180000349951<span class="Apple-tab-span" style="white-space:pre"> </span>maker<span class="Apple-tab-span" style="white-space:pre"> </span>CDS<span class="Apple-tab-span" style="white-space:pre"> </span>98033<span class="Apple-tab-span" style="white-space:pre"> </span>98140<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=PB12301-RA:cds:10114;Parent=PB12301-RA;</div>
<div>pbar_scf7180000349951<span class="Apple-tab-span" style="white-space:pre"> </span>maker<span class="Apple-tab-span" style="white-space:pre"> </span>CDS<span class="Apple-tab-span" style="white-space:pre"> </span>98393<span class="Apple-tab-span" style="white-space:pre"> </span>98530<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=PB12301-RA:cds:10113;Parent=PB12301-RA;</div>
</div><div><br></div><div>output:</div><div><br></div><div><div>pbar_scf7180000349951<span class="Apple-tab-span" style="white-space:pre"> </span>maker<span class="Apple-tab-span" style="white-space:pre"> </span>mRNA<span class="Apple-tab-span" style="white-space:pre"> </span>98033<span class="Apple-tab-span" style="white-space:pre"> </span>98530<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=PB12301-RA;Parent=PB12301;Name=PB12301-RA;_AED=0.38;_eAED=0.38;_QI=0|0|0.33|1|0.5|1|3|246|165;Alias=genemark-pbar_scf7180000349951-abinit-gene-1.14-mRNA-1,PB12301-RA</div>
<div>pbar_scf7180000349951<span class="Apple-tab-span" style="white-space:pre"> </span>maker<span class="Apple-tab-span" style="white-space:pre"> </span>exon<span class="Apple-tab-span" style="white-space:pre"> </span>98033<span class="Apple-tab-span" style="white-space:pre"> </span>98530<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=PB12301-RA:exon:134;Parent=PB12301-RA</div>
<div>pbar_scf7180000349951<span class="Apple-tab-span" style="white-space:pre"> </span>maker<span class="Apple-tab-span" style="white-space:pre"> </span>exon<span class="Apple-tab-span" style="white-space:pre"> </span>98033<span class="Apple-tab-span" style="white-space:pre"> </span>98140<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=PB12301-RA:exon:133;Parent=PB12301-RA</div>
<div>pbar_scf7180000349951<span class="Apple-tab-span" style="white-space:pre"> </span>maker<span class="Apple-tab-span" style="white-space:pre"> </span>exon<span class="Apple-tab-span" style="white-space:pre"> </span>98393<span class="Apple-tab-span" style="white-space:pre"> </span>98530<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=PB12301-RA:exon:132;Parent=PB12301-RA</div>
<div>pbar_scf7180000349951<span class="Apple-tab-span" style="white-space:pre"> </span>maker<span class="Apple-tab-span" style="white-space:pre"> </span>three_prime_UTR<span class="Apple-tab-span" style="white-space:pre"> </span>98393<span class="Apple-tab-span" style="white-space:pre"> </span>98530<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=PB12301-RA:three_prime_utr;Parent=PB12301-RA</div>
<div>pbar_scf7180000349951<span class="Apple-tab-span" style="white-space:pre"> </span>maker<span class="Apple-tab-span" style="white-space:pre"> </span>three_prime_UTR<span class="Apple-tab-span" style="white-space:pre"> </span>98033<span class="Apple-tab-span" style="white-space:pre"> </span>98140<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=PB12301-RA:three_prime_utr;Parent=PB12301-RA</div>
<div>pbar_scf7180000349951<span class="Apple-tab-span" style="white-space:pre"> </span>maker<span class="Apple-tab-span" style="white-space:pre"> </span>CDS<span class="Apple-tab-span" style="white-space:pre"> </span>98033<span class="Apple-tab-span" style="white-space:pre"> </span>98530<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=PB12301-RA:cds;Parent=PB12301-RA</div>
</div><div><br></div><div>Thank you,</div><div><br></div><div>Sasha<br><br><div class="gmail_quote">On Tue, Mar 12, 2013 at 10:37 PM, Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word"><div>Yes. Try the newer version and see if you still have the issue.</div>
<div><br></div><div>Thanks,</div><div>Carson</div><div><br></div><div><br></div><span><div style="border-right:medium none;padding-right:0in;padding-left:0in;padding-top:3pt;text-align:left;font-size:11pt;border-bottom:medium none;font-family:Calibri;border-top:#b5c4df 1pt solid;padding-bottom:0in;border-left:medium none">
<span style="font-weight:bold">From: </span> Sasha Mikheyev <<a href="mailto:mikheyev@gmail.com" target="_blank">mikheyev@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Tuesday, 12 March, 2013 1:26 AM<br>
<span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Cc: </span> Barry Moore <<a href="mailto:barry.moore@genetics.utah.edu" target="_blank">barry.moore@genetics.utah.edu</a>>, <<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>><div>
<div><br><span style="font-weight:bold">Subject: </span> Re: [maker-devel] duplicate CDS in annotation<br></div></div></div><div><div><div><br></div>Hi Carson,<div><br></div><div>I have been using version 2.10. Is it worth trying with a newer version?</div>
<div><br></div><div>You can find the model file <a href="https://dl.dropbox.com/u/5275622/all.gff.gz" target="_blank">here</a>. It is rather large, as it includes all of the output from the first maker run.</div><div><br>
</div><div>Yours,</div><div><br>Sasha</div><div><br><br><div class="gmail_quote">On Mon, Mar 11, 2013 at 10:02 PM, Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word"><div>I think the issue is that you are getting a match feature that is being printed with the same ID as the mRNA feature. Correct?</div>
<div><br></div><div>What version of MAKER are you using, and what does the gile you are giving to pred_gff or model_gff look like? Could you send them?</div><div><br></div><div>Thanks,</div><div>Carson</div><div><br></div>
<div><br></div><span><div style="border-right:medium none;padding-right:0in;padding-left:0in;padding-top:3pt;text-align:left;font-size:11pt;border-bottom:medium none;font-family:Calibri;border-top:#b5c4df 1pt solid;padding-bottom:0in;border-left:medium none">
<span style="font-weight:bold">From: </span> Barry Moore <<a href="mailto:barry.moore@genetics.utah.edu" target="_blank">barry.moore@genetics.utah.edu</a>><br><span style="font-weight:bold">Date: </span> Monday, 11 March, 2013 7:32 AM<br>
<span style="font-weight:bold">To: </span> Sasha Mikheyev <<a href="mailto:mikheyev@gmail.com" target="_blank">mikheyev@gmail.com</a>><br><span style="font-weight:bold">Cc: </span> <<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>><br>
<span style="font-weight:bold">Subject: </span> Re: [maker-devel] duplicate CDS in annotation<br></div><div><div><div><br></div><div><div style="word-wrap:break-word">Hi Sasha,<div><br></div><div>This gene model appears to be correctly formatted to me. In GFF3 format the CDS features are allowed to span multiple lines and they share the same ID to indicate that it is all the same features. See the GFF3 specification on the Sequence Ontology website (<a href="http://www.sequenceontology.org/resources/gff3.html" target="_blank">http://www.sequenceontology.org/resources/gff3.html</a>), and in particular the description of the ID attribute specifies:</div>
<div><br></div><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div>ID Indicates the ID of the feature. IDs for each feature must be unique
within the scope of the GFF file. In the case of discontinuous
features (i.e. a single feature that exists over multiple genomic
locations) the same ID may appear on multiple lines. All lines that
share an ID collectively represent a single feature. </div></blockquote><div><span></span></div><div><br></div><div>So each of those CDS lines forms one part of the single CDS feature for this gene.</div><div><br></div><div>
B</div><div> <br><div><div>On Mar 11, 2013, at 3:46 AM, Sasha Mikheyev wrote:</div><br><blockquote type="cite"><div>Dear Yandell lab,</div><div><br></div><div>I am re-annotating the harvester and genome using protein and RNA-seq data. However, I get many artifacts like the one below. It seems that there are several CDS records that should tie in to the same mRNA, but they are really hanging out separately, and produce several nucleotide sequences with the same name when extracted from the gff. I would appreciate any guidance about how to fix this!</div>
<div><br></div><div>Thank you,</div><div><br></div><div>Sasha</div><div><br></div><div>grep "pbar_scf7180000350377:hit:2506" Pbar.2.0.gff </div><div>pbar_scf7180000350377<span style="white-space:pre-wrap"> </span>protein2genome<span style="white-space:pre-wrap"> </span>protein_match<span style="white-space:pre-wrap"> </span>172004<span style="white-space:pre-wrap"> </span>172162<span style="white-space:pre-wrap"> </span>150<span style="white-space:pre-wrap"> </span>-<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>ID=pbar_scf7180000350377:hit:2506;Name=Hsal|HS9704;score=150;</div>
<div>pbar_scf7180000350377<span style="white-space:pre-wrap"> </span>protein2genome<span style="white-space:pre-wrap"> </span>match_part<span style="white-space:pre-wrap"> </span>172004<span style="white-space:pre-wrap"> </span>172162<span style="white-space:pre-wrap"> </span>150<span style="white-space:pre-wrap"> </span>-<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>ID=pbar_scf7180000350377:hsp:2798;Parent=pbar_scf7180000350377:hit:2506;Name=Hsal|HS9704;Target=Hsal|HS9704 1 53 +;Gap=M159;</div>
<div>pbar_scf7180000350377<span style="white-space:pre-wrap"> </span>maker<span style="white-space:pre-wrap"> </span>mRNA<span style="white-space:pre-wrap"> </span>538308<span style="white-space:pre-wrap"> </span>558769<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>+<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>ID=pbar_scf7180000350377:hit:2506;Parent=augustus_masked-pbar_scf7180000350377-abinit-gene-5.29;Name=augustus_masked-pbar_scf7180000350377-abinit-gene-5.29-mRNA-1;_AED=0.48;_eAED=0.39;_QI=0|0|0|0.5|1|1|6|0|395;score=0.01;</div>
<div>pbar_scf7180000350377<span style="white-space:pre-wrap"> </span>maker<span style="white-space:pre-wrap"> </span>exon<span style="white-space:pre-wrap"> </span>538308<span style="white-space:pre-wrap"> </span>538334<span style="white-space:pre-wrap"> </span>0.01<span style="white-space:pre-wrap"> </span>+<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>ID=pbar_scf7180000350377:hit:2506:exon:305;Parent=pbar_scf7180000350377:hit:2506;</div>
<div>pbar_scf7180000350377<span style="white-space:pre-wrap"> </span>maker<span style="white-space:pre-wrap"> </span>exon<span style="white-space:pre-wrap"> </span>538748<span style="white-space:pre-wrap"> </span>538968<span style="white-space:pre-wrap"> </span>0.01<span style="white-space:pre-wrap"> </span>+<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>ID=pbar_scf7180000350377:hit:2506:exon:306;Parent=pbar_scf7180000350377:hit:2506;</div>
<div>pbar_scf7180000350377<span style="white-space:pre-wrap"> </span>maker<span style="white-space:pre-wrap"> </span>exon<span style="white-space:pre-wrap"> </span>539842<span style="white-space:pre-wrap"> </span>540242<span style="white-space:pre-wrap"> </span>0.01<span style="white-space:pre-wrap"> </span>+<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>ID=pbar_scf7180000350377:hit:2506:exon:307;Parent=pbar_scf7180000350377:hit:2506;</div>
<div>pbar_scf7180000350377<span style="white-space:pre-wrap"> </span>maker<span style="white-space:pre-wrap"> </span>exon<span style="white-space:pre-wrap"> </span>542624<span style="white-space:pre-wrap"> </span>542798<span style="white-space:pre-wrap"> </span>0.01<span style="white-space:pre-wrap"> </span>+<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>ID=pbar_scf7180000350377:hit:2506:exon:308;Parent=pbar_scf7180000350377:hit:2506;</div>
<div>pbar_scf7180000350377<span style="white-space:pre-wrap"> </span>maker<span style="white-space:pre-wrap"> </span>exon<span style="white-space:pre-wrap"> </span>555823<span style="white-space:pre-wrap"> </span>556025<span style="white-space:pre-wrap"> </span>0.01<span style="white-space:pre-wrap"> </span>+<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>ID=pbar_scf7180000350377:hit:2506:exon:309;Parent=pbar_scf7180000350377:hit:2506;</div>
<div>pbar_scf7180000350377<span style="white-space:pre-wrap"> </span>maker<span style="white-space:pre-wrap"> </span>exon<span style="white-space:pre-wrap"> </span>558609<span style="white-space:pre-wrap"> </span>558769<span style="white-space:pre-wrap"> </span>0.01<span style="white-space:pre-wrap"> </span>+<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>ID=pbar_scf7180000350377:hit:2506:exon:310;Parent=pbar_scf7180000350377:hit:2506;</div>
<div>pbar_scf7180000350377<span style="white-space:pre-wrap"> </span>maker<span style="white-space:pre-wrap"> </span>CDS<span style="white-space:pre-wrap"> </span>538308<span style="white-space:pre-wrap"> </span>538334<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>+<span style="white-space:pre-wrap"> </span>0<span style="white-space:pre-wrap"> </span>ID=pbar_scf7180000350377:hit:2506:cds:305;Parent=pbar_scf7180000350377:hit:2506;</div>
<div>pbar_scf7180000350377<span style="white-space:pre-wrap"> </span>maker<span style="white-space:pre-wrap"> </span>CDS<span style="white-space:pre-wrap"> </span>538748<span style="white-space:pre-wrap"> </span>538968<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>+<span style="white-space:pre-wrap"> </span>0<span style="white-space:pre-wrap"> </span>ID=pbar_scf7180000350377:hit:2506:cds:306;Parent=pbar_scf7180000350377:hit:2506;</div>
<div>pbar_scf7180000350377<span style="white-space:pre-wrap"> </span>maker<span style="white-space:pre-wrap"> </span>CDS<span style="white-space:pre-wrap"> </span>539842<span style="white-space:pre-wrap"> </span>540242<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>+<span style="white-space:pre-wrap"> </span>1<span style="white-space:pre-wrap"> </span>ID=pbar_scf7180000350377:hit:2506:cds:307;Parent=pbar_scf7180000350377:hit:2506;</div>
<div>pbar_scf7180000350377<span style="white-space:pre-wrap"> </span>maker<span style="white-space:pre-wrap"> </span>CDS<span style="white-space:pre-wrap"> </span>542624<span style="white-space:pre-wrap"> </span>542798<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>+<span style="white-space:pre-wrap"> </span>2<span style="white-space:pre-wrap"> </span>ID=pbar_scf7180000350377:hit:2506:cds:308;Parent=pbar_scf7180000350377:hit:2506;</div>
<div>pbar_scf7180000350377<span style="white-space:pre-wrap"> </span>maker<span style="white-space:pre-wrap"> </span>CDS<span style="white-space:pre-wrap"> </span>555823<span style="white-space:pre-wrap"> </span>556025<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>+<span style="white-space:pre-wrap"> </span>1<span style="white-space:pre-wrap"> </span>ID=pbar_scf7180000350377:hit:2506:cds:309;Parent=pbar_scf7180000350377:hit:2506;</div>
<div>pbar_scf7180000350377<span style="white-space:pre-wrap"> </span>maker<span style="white-space:pre-wrap"> </span>CDS<span style="white-space:pre-wrap"> </span>558609<span style="white-space:pre-wrap"> </span>558769<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>+<span style="white-space:pre-wrap"> </span>2<span style="white-space:pre-wrap"> </span>ID=pbar_scf7180000350377:hit:2506:cds:310;Parent=pbar_scf7180000350377:hit:2506;</div>
<div><br></div>
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</blockquote></div><br><div><div><span style="font-family:Arial;font-size:12px"><div>Barry Moore</div><div>Research Scientist</div><div>Dept. of Human Genetics</div><div>University of Utah</div><div>Salt Lake City, UT 84112</div>
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