[Gramene] Fwd: [Eg_internal] Fwd: Maize genome on Ensemble repository

[Dan Bolser]

Hi Gramene!

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?"

I've already summarised details about biotype and analysis regarding gene
counts.


Many thanks,
Dan.

---------- Forwarded message ----------
From: Noushin Ghaffari <nghaffari at tamu.edu>
Date: 2 October 2013 21:25
Subject: Re: [Eg_internal] Fwd: Maize genome on Ensemble repository
To: Dan Bolser <dbolser at ebi.ac.uk>
Cc: "Dr. Lisa Vaillancourt" <vaillan at uky.edu>, Charlie Johnson <
charlie at ag.tamu.edu>


 Hi Dan,

 Thank you for pointing me to the GFF file, that was very helpful! No
wonder I couldn't find it, it's pretty hidden in Ensembel's FTP site.

 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?

 Thank you very much,
Noushin


 ------------------------------------------------------
 Noushin Ghaffari, PhD
 Bioinformatics Scientist
 AgriLife Genomics and Bioinformatics Services
 Texas AgriLife Research
 Texas A&M System
 College Station, TX  77843-2123

 Email: nghaffari at tamu.edu
 Phone: 979-862-2784 <tel:979-862-2784>
 Office: 176B - Norman E. Borlaug Center





 On 10/1/13 3:00 AM, "Dan Bolser" <dbolser at ebi.ac.uk> wrote:

 Hi Noushin, thanks for your enquiry.

 I think you're right, we should link to the GFF dumps more clearly!
However, you can find what you need here:
ftp://ftp.ensemblgenomes.org/pub/plants/release-20/gff3/zea_mays/


 Many thanks,
Dan.

 On 1 October 2013 08:53, Paul Kersey <pkersey at ebi.ac.uk> wrote:

Hello
can we deal with this through the helpdesk?  probably to be passed onto Dan
B.
thanks
P.

 Begin forwarded message:

 From: Noushin Ghaffari <nghaffari at tamu.edu>
Subject: Maize genome on Ensemble repository
Date: 30 September 2013 21:47:23 BST
To: "pkersey at ebi.ac.uk" <pkersey at ebi.ac.uk>
Cc: "Dr. Lisa Vaillancourt" <vaillan at uky.edu>, Charlie Johnson
<charlie at ag.tamu.edu>

 Dear Paul,

 This is Noushin from Texas A&M University. I am working on a collaborating
project with University of Kentucky, which invloves maize. I have used the
older corn genome, RefGen_v2, which was provided by:
http://maizesequence.org/Zea_mays/Info/StatsTable?db=core

 I used the GFF file associated with the FASTA files of the chromosomes for
annotation, in order to map the reads to the reference genomes.

 Our team is very excited about the release of the new maize reference
genome, RefGen_V3 by Ensemble! However, I cannot find the GFF file anywhere
to annotate the reference genome! From the statistics page of the genome I
can see that there are ~63K coding genes (compared to ~39K filtered genes in
the previous release), and I can find the genes, cdna and rrna files for
each chromosome with lots of useful information, but as a bioinformatician,
I would need to find a GFF file that can annotate the chromosomes. I truly
appreciate if you can assist me in this matter.

 Thank you for your time and assistance in advance.

 Best,
Noushin


 ------------------------------------------------------
Noushin Ghaffari, PhD
Bioinformatics Scientist
AgriLife Genomics and Bioinformatics Services
Texas AgriLife Research
Texas A&M System
College Station, TX  77843-2123

 Email: nghaffari at tamu.edu
Phone: 979-862-2784
Office: 176B - Norman E. Borlaug Center


 ---
Dr. Paul Kersey
Team Leader, Non-vertebrate Genomics
European Bioinformatics Institute
European Molecular Biology Laboratory           Tel: +44-(0)1223-494601
Wellcome Trust Genome Campus, Hinxton      Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK                                   email:
pkersey at ebi.ac.uk




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