<div dir="ltr">Hi Gramene!<div><br></div><div>Can you answer the question below about: "Should I go ahead and use this newly released set in my analysis or your team expects an update for this release in a very short timeframe?"</div>
<div><br></div><div>I've already summarised details about biotype and analysis regarding gene counts.</div><div><br></div><div><br></div><div>Many thanks,</div><div>Dan.<br><div><br></div><div class="gmail_quote">---------- Forwarded message ----------<br>
From: <b class="gmail_sendername">Noushin Ghaffari</b> <span dir="ltr"><<a href="mailto:nghaffari@tamu.edu">nghaffari@tamu.edu</a>></span><br>Date: 2 October 2013 21:25<br>Subject: Re: [Eg_internal] Fwd: Maize genome on Ensemble repository<br>
To: Dan Bolser <<a href="mailto:dbolser@ebi.ac.uk">dbolser@ebi.ac.uk</a>><br>Cc: "Dr. Lisa Vaillancourt" <<a href="mailto:vaillan@uky.edu">vaillan@uky.edu</a>>, Charlie Johnson <<a href="mailto:charlie@ag.tamu.edu">charlie@ag.tamu.edu</a>><br>
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<div style><font>Hi Dan,</font></div>
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<div>T<font style>hank you for pointing me to the GFF file, that was very helpful! N</font><font>o wonder I couldn't find it, it's pretty hidden in Ensembel's FTP site.</font></div>
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<div><font>I will use the set of "_rm_" genes, which my understanding is that they are gone through the Repeat Masking and filtering. However, in the new release there are ~63K genes and in the previous maize reference genome (in the working set) there were
~39K genes. I am guessing the difference is in the predicted and not curated genes. Should I go ahead and use this newly released set in my analysis or your team expects an update for this release in a very short timeframe?</font></div>
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<div><font>Thank you very much,</font></div><div class="im">
<div><font>Noushin</font></div>
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<div style="font-size:14px;font-family:Calibri,sans-serif">
<font face="Consolas,monospace">Noushin Ghaffari, PhD</font></div>
<div style="font-size:14px;font-family:Calibri,sans-serif">
<font face="Consolas,monospace">Bioinformatics Scientist</font></div>
<div style="font-size:14px;font-family:Calibri,sans-serif">
<font face="Consolas,monospace">AgriLife Genomics and Bioinformatics Services</font></div>
<div style="font-size:14px;font-family:Calibri,sans-serif">
<font face="Consolas,monospace">Texas AgriLife Research</font></div>
<div style="font-size:14px;font-family:Calibri,sans-serif">
<font face="Consolas,monospace">Texas A&M System</font></div>
<div style="font-size:14px;font-family:Calibri,sans-serif">
<font face="Consolas,monospace">College Station, TX 77843-2123</font></div>
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<font face="Consolas,monospace">Email: <a href="mailto:nghaffari@tamu.edu" target="_blank">nghaffari@tamu.edu</a></font></div>
</div><div style="font-size:14px;font-family:Calibri,sans-serif">
<font face="Consolas,monospace">Phone: 979-862-2784 <tel:979-862-2784></font></div><div class="im">
<div style="font-size:14px;font-family:Calibri,sans-serif">
<font face="Consolas,monospace">Office: 176B - Norman E. Borlaug Center</font></div>
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On 10/1/13 3:00 AM, "Dan Bolser" <<a href="mailto:dbolser@ebi.ac.uk" target="_blank">dbolser@ebi.ac.uk</a>> wrote:</div>
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<div>Hi Noushin, thanks for your enquiry.</div>
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<div>I think you're right, we should link to the GFF dumps more clearly!</div>
<div>However, you can find what you need here:</div>
<div><a href="ftp://ftp.ensemblgenomes.org/pub/plants/release-20/gff3/zea_mays/" target="_blank">ftp://ftp.ensemblgenomes.org/pub/plants/release-20/gff3/zea_mays/</a></div>
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<div>Many thanks,</div>
<div>Dan.</div>
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<div>On 1 October 2013 08:53, Paul Kersey <<a href="mailto:pkersey@ebi.ac.uk" target="_blank">pkersey@ebi.ac.uk</a>> wrote:</div>
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<div>Hello</div>
<div>can we deal with this through the helpdesk? probably to be passed onto Dan</div>
<div>B.</div>
<div>thanks</div>
<div>P.</div>
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<div>Begin forwarded message:</div>
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<div>From: Noushin Ghaffari <<a href="mailto:nghaffari@tamu.edu" target="_blank">nghaffari@tamu.edu</a>></div>
<div>Subject: Maize genome on Ensemble repository</div>
<div>Date: 30 September 2013 21:47:23 BST</div>
<div>To: "<a href="mailto:pkersey@ebi.ac.uk" target="_blank">pkersey@ebi.ac.uk</a>" <<a href="mailto:pkersey@ebi.ac.uk" target="_blank">pkersey@ebi.ac.uk</a>></div>
<div>Cc: "Dr. Lisa Vaillancourt" <<a href="mailto:vaillan@uky.edu" target="_blank">vaillan@uky.edu</a>>, Charlie Johnson</div>
<div><<a href="mailto:charlie@ag.tamu.edu" target="_blank">charlie@ag.tamu.edu</a>></div>
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<div>Dear Paul,</div>
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<div>This is Noushin from Texas A&M University. I am working on a collaborating</div>
<div>project with University of Kentucky, which invloves maize. I have used the</div>
<div>older corn genome, RefGen_v2, which was provided by:</div>
<div><a href="http://maizesequence.org/Zea_mays/Info/StatsTable?db=core" target="_blank">http://maizesequence.org/Zea_mays/Info/StatsTable?db=core</a></div>
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<div>I used the GFF file associated with the FASTA files of the chromosomes for</div>
<div>annotation, in order to map the reads to the reference genomes.</div>
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<div>Our team is very excited about the release of the new maize reference</div>
<div>genome, RefGen_V3 by Ensemble! However, I cannot find the GFF file anywhere</div>
<div>to annotate the reference genome! From the statistics page of the genome I</div>
<div>can see that there are ~63K coding genes (compared to ~39K filtered genes in</div>
<div>the previous release), and I can find the genes, cdna and rrna files for</div>
<div>each chromosome with lots of useful information, but as a bioinformatician,</div>
<div>I would need to find a GFF file that can annotate the chromosomes. I truly</div>
<div>appreciate if you can assist me in this matter.</div>
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<div>Thank you for your time and assistance in advance.</div>
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<div>Best,</div>
<div>Noushin</div>
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<div>------------------------------------------------------</div>
<div>Noushin Ghaffari, PhD</div>
<div>Bioinformatics Scientist</div>
<div>AgriLife Genomics and Bioinformatics Services</div>
<div>Texas AgriLife Research</div>
<div>Texas A&M System</div>
<div>College Station, TX 77843-2123</div>
<div><br>
</div>
<div>Email: <a href="mailto:nghaffari@tamu.edu" target="_blank">nghaffari@tamu.edu</a></div>
<div>Phone: 979-862-2784</div>
<div>Office: 176B - Norman E. Borlaug Center</div>
<div><br>
</div>
<div><br>
</div>
<div>---</div>
<div>Dr. Paul Kersey</div>
<div>Team Leader, Non-vertebrate Genomics</div>
<div>European Bioinformatics Institute</div>
<div>European Molecular Biology Laboratory Tel: <a href="tel:%2B44-%280%291223-494601" value="+441223494601" target="_blank">+44-(0)1223-494601</a></div>
<div>Wellcome Trust Genome Campus, Hinxton Fax: <a href="tel:%2B44-%280%291223-494468" value="+441223494468" target="_blank">+44-(0)1223-494468</a></div>
<div>Cambridge CB10 1SD, UK email:</div>
<div><a href="mailto:pkersey@ebi.ac.uk" target="_blank">pkersey@ebi.ac.uk</a></div>
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