From kclark at cshl.edu  Wed Oct  2 10:01:26 2013
From: kclark at cshl.edu (kclark at cshl.edu)
Date: Wed, 2 Oct 2013 10:01:26 -0400
Subject: [Gramene] [Website feedback] hi there
Message-ID: <201310021401.r92E1Q4N023305@brie.cshl.edu>

kclark (http://brie.cshl.edu/drupal/?q=user/1) sent a message using the
contact form at http://brie.cshl.edu/drupal/?q=contact.

i love you


From dbolser at ebi.ac.uk  Thu Oct  3 05:02:37 2013
From: dbolser at ebi.ac.uk (Dan Bolser)
Date: Thu, 3 Oct 2013 10:02:37 +0100
Subject: [Gramene] Fwd: [Eg_internal] Fwd: Maize genome on Ensemble
	repository
In-Reply-To: <ed2c527e-3b1c-4591-8b67-cd18f8cf7849@MAILCASH02.agnet.tamu.edu>
References: <CAP+7WGyhcPzPoa+P0duvDgunqRyxH4SDdDmweHFZjXDAZG+V0Q@mail.gmail.com>
	<ed2c527e-3b1c-4591-8b67-cd18f8cf7849@MAILCASH02.agnet.tamu.edu>
Message-ID: <CAP+7WGxpCMBgUixhb0gD+Aa7ZuBZU-nstJrFTWXWJc7kKHDCZw@mail.gmail.com>

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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Eg_internal mailing list
Eg_internal at ebi.ac.uk
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From wangch16 at 126.com  Thu Oct 17 04:51:17 2013
From: wangch16 at 126.com (wangch16)
Date: Thu, 17 Oct 2013 16:51:17 +0800 (CST)
Subject: [Gramene] Can I submit data/maps to Gramene
Message-ID: <4ddcdc12.108c7.141c59c9c31.Coremail.wangch16@126.com>

Dear,
I have some allelic information about microsatellite, and want to submit these data to Gramene. How can I do?



Sincerely yours,

Caihong Wang
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From rpetry at ebi.ac.uk  Thu Oct 17 06:50:37 2013
From: rpetry at ebi.ac.uk (Robert Petryszak)
Date: Thu, 17 Oct 2013 11:50:37 +0100
Subject: [Gramene] Fwd: Re: collaboration with ATLAS on sharing plant data
 on ensembl browser (Attn: Paul Kersey and Doreen)
In-Reply-To: <CAP+7WGyBWnTGC92mOCMp1erQZJZZguBxUrh7__R7JJ0LgUOG5A@mail.gmail.com>
References: <CAP+7WGyBWnTGC92mOCMp1erQZJZZguBxUrh7__R7JJ0LgUOG5A@mail.gmail.com>
Message-ID: <525FC0FD.3040709@ebi.ac.uk>

Dear Gramene Folks,

I am experimenting with attaching a track from a bedGraph file to both 
Gramene and Ensembl Plants Genome browsers. I've had success with a 
Ensembl Plants browser, but not with Gramene browser, e.g.

http://www.gramene.org/Oryza_sativa/Location/View?db=core;g=OS12G0136500;r=12:1761563-1811562;t=OS12T0136500-01;contigviewbottom=url:http://www.ebi.ac.uk/~rpetry/irap/E-MTAB-1625_oryza_sativa_japonica_group/E-MTAB-1625/tophat1/htseq2/deseq/growth_condition_normal_watering_at_24_hours_vs_5_hours.genes_de.fold.bedGraph;format=bedGraph

The info on the page says that the track is attached, but the track data 
is missing. Would you happen to know what is causing it?

Thanks for your help in advance.

Kind regards,

Robert.

Robert Petryszak
Expression Atlas Co-ordinator
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Tel: +44 (0)1223 492 696
Skype: rpetryszak
http://www.ebi.ac.uk/services/teams/expression-atlas




-------- Original Message --------
Subject: 	Re: collaboration with ATLAS on sharing plant data on ensembl 
browser (Attn: Paul Kersey and Doreen)
Date: 	Thu, 17 Oct 2013 11:43:14 +0100
From: 	Dan Bolser <dbolser at ebi.ac.uk>
To: 	rpetry at ebi.ac.uk
CC: 	Paul Kersey <pkersey at ebi.ac.uk>, Dan Bolser <dbolser at ebi.ac.uk>, 
Maria Keays <mkeays at ebi.ac.uk>, Helen Parkinson <parkinson at ebi.ac.uk>, 
Nuno Fonseca <nf at ebi.ac.uk>



Hi Robert,

It's possible that Gramene haven't installed the appropriate module of
the web-code used to render the BED format. It's probably best to ask
them directly. You can use this address for general questions that
should get directed through to the right person:
gramene at gramene.org

The track looks great in EG btw!


Many thanks,
Dan.

On 16 October 2013 18:10, Robert Petryszak <rpetry at ebi.ac.uk> wrote:
> Paul, Dan,
>
> We've started some experiments on attaching tracks to Ensembl Plants and
> Gramene genome browsers. At this stage I feel it will be more effective to
> get answers from you on some specific questions.
>
> I've managed to attach a fold change track from one of our Gramene rice
> experiments to the Ensembl Plants genome browser:
>
> http://plants.ensembl.org/Oryza_sativa/Location/View?db=core;g=OS12G0136500;r=12:1761563-1811562;t=OS12T0136500-01;contigviewbottom=url:http://www.ebi.ac.uk/~rpetry/irap/E-MTAB-1625_oryza_sativa_japonica_group/E-MTAB-1625/tophat1/htseq2/deseq/growth_condition_normal_watering_at_24_hours_vs_5_hours.genes_de.fold.bedGraph;format=bedGraph
>
> However, having tried the same on the Gramene browser, I can see an info on
> the page below that the track was attached, but cannot see the actual track
> data:
>
> http://www.gramene.org/Oryza_sativa/Location/View?db=core;g=OS12G0136500;r=12:1761563-1811562;t=OS12T0136500-01;contigviewbottom=url:http://www.ebi.ac.uk/~rpetry/irap/E-MTAB-1625_oryza_sativa_japonica_group/E-MTAB-1625/tophat1/htseq2/deseq/growth_condition_normal_watering_at_24_hours_vs_5_hours.genes_de.fold.bedGraph;format=bedGraph
>
> Would you happen to know what might be causing this?
>
> Many thanks for your help.
>
> Best wishes,
>
> Robert.
>
>
> On 30/09/2013 14:44, Robert Petryszak wrote:
>
> Ok, thanks Paul - let's pencil that in - I'll confim again as soon as Nuno
> is back from holiday.
>
> Cheers,
>
> Robert.
>
>
> On 30/09/2013 14:37, Paul Kersey wrote:
>
>
> On 30 Sep 2013, at 14:36, Robert Petryszak <rpetry at ebi.ac.uk> wrote:
>
> Hi All,
>
> We have to do some ground work on the iRAP side (RNA-seq processing pipeline
> we use) before for the meeting to be productive for us.
> Nuno Fonseca will need to be there also, but he is away this week, and I'm
> away most of the next. It would make sense to schedule the meeting from 14th
> Oct onwards. Paul, when are you around that week?
>
>
> only on Friday 18th.
>
> P.
>
>
> Thanks,
>
> Robert.
>
>
> On 30/09/2013 14:33, Paul Kersey wrote:
>
> how about meeting on Thursday @ 11.00?  We can have a follow up meeting with
> Helen later if necessary.
> As there will be just 4 of us, we can meet in my office.
>
> P.
>
> On 30 Sep 2013, at 14:30, Maria Keays <mkeays at ebi.ac.uk> wrote:
>
> Hello,
>
> I'm free any time this week but on holiday all next week.
>
> Thanks,
> Maria
>
>
> On 30/09/2013 14:26, Helen Parkinson wrote:
>
> 1. Display gene expression data vs. Ensembl genomes for the Gramene project
> 2. Design a process for this.
>
> Helen.
> On 30/09/2013 14:25, Paul Kersey wrote:
>
> I'm also around the following week, Mon, Tue AM, Wed PM, and Thu.
> I guess someone needs to be at the meeting who knows what the objective is
> here (it isn't me, I don't know if that's you?)
> P.
>
>
> On 30 Sep 2013, at 14:18, Helen Parkinson <parkinson at ebi.ac.uk
> <mailto:parkinson at ebi.ac.uk>> wrote:
>
> Hi Paul
>
> Robert and Maria are the relevant people. I am off to Bar Harbor this week,
> so next would be better if I am needed
>
> cheers
>
> Helen
>
> On 30/09/2013 13:49, Paul Kersey wrote:
>
> Hi Helen
>
> i'm about most of this week, do you want to drop by (or send someone from
> your team) for a preliminary discussion?
>
> P.
>
> On 25 Sep 2013, at 21:51, Helen Parkinson <parkinson at ebi.ac.uk
> <mailto:parkinson at ebi.ac.uk> <mailto:parkinson at ebi.ac.uk>> wrote:
>
> Hi Paul
>
> we can come and see you and relevant colleagues in person if that makes it
> easier and then hold a conf. call. We'd like to get a timeline set for the
> next 6 months and now seemed like a good time, as we have curated and loaded
> a lot of data,
>
> best wishes
>
> Helen
> On 25/09/2013 21:49, Pankaj Jaiswal (OSU) wrote:
>
> Hi Paul and Doreen,
>
> Helen's ATLAS group and my group at OSU met today to discuss progress on the
> Gramene-ATLAS collaboration. A number of microarray based gene expression
> studies have been analyzed and loaded in the ATLAS by Helen's group. This
> work will continue to progress. In the mean time, we have also developed a
> workflow for analyzing the RNA-Seq data and working on refining it along
> with the outputs for user interfaces e.g. the one listed here
> http://www-test.ebi.ac.uk/gxa/experiments/E-MTAB-1625?accessKey=49bbc834-148f-4319-904b-a044fb99603d.
> This is still a private data that we generated that is being used to develop
> the workflow and user interfaces.
>
> With this reference we are looking towards working with your groups and
> experts to display this data on the genome browsers running at Ensembl
> Plants and Gramene. I am not sure which of these options
> (Webservices/data_files/integration_in_the_db) is a good one that is
> currently being used by the Human Ensembl. Either way, I think this is the
> right time to discuss it.
>
> Please let me know if you would like to discuss it via a conference call.
> Doreen let me know who can be the lead from your group on this discussion.
>
> Best
> Pankaj
>
>
>
> --
> Helen Parkinson, PhD
> Team Leader
> Samples Phenotypes and Ontologies Team
> -------------------------------------------
> European Bioinformatics Institute (EMBL-EBI)
> European Molecular Biology Laboratory
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge CB10 1SD
> United Kingdom
>
> EBI 01223 494672
> Skype: helen.parkinson.ebi
> www.ebi.ac.uk/fgpt/ <http://www.ebi.ac.uk/fgpt/>
> <http://www.ebi.ac.uk/fgpt/>
>
>
> ---
> 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 <mailto:pkersey at ebi.ac.uk>
> <mailto:pkersey at ebi.ac.uk>
>
>
>
>
> --
> Helen Parkinson, PhD
> Team Leader
> Samples Phenotypes and Ontologies Team
> -------------------------------------------
> European Bioinformatics Institute (EMBL-EBI)
> European Molecular Biology Laboratory
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge CB10 1SD
> United Kingdom
>
> EBI 01223 494672
> Skype: helen.parkinson.ebi
> www.ebi.ac.uk/fgpt/ <http://www.ebi.ac.uk/fgpt/>
>
>
> ---
> 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 <mailto:pkersey at ebi.ac.uk>
>
>
>
>
>
> --
> Maria Keays
> Functional Genomics
> European Bioinformatics Institute (EMBL-EBI)
> European Molecular Biology Laboratory
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge CB10 1SD
> United Kingdom
> Tel: +44 (0)1223 494546
>
>
> ---
> 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
>
>
>
>
>
> --
> Robert Petryszak
> Expression Atlas Co-ordinator
> European Bioinformatics Institute (EMBL-EBI)
> European Molecular Biology Laboratory
> Tel: +44 (0)1223 492 696
> Skype: rpetryszak
> http://www.ebi.ac.uk/services/teams/expression-atlas
>
>
> ---
> 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
>
>
>
>
>
> --
> Robert Petryszak
> Expression Atlas Co-ordinator
> European Bioinformatics Institute (EMBL-EBI)
> European Molecular Biology Laboratory
> Tel: +44 (0)1223 492 696
> Skype: rpetryszak
> http://www.ebi.ac.uk/services/teams/expression-atlas
>
>
>
> --
> Robert Petryszak
> Expression Atlas Co-ordinator
> European Bioinformatics Institute (EMBL-EBI)
> European Molecular Biology Laboratory
> Tel: +44 (0)1223 492 696
> Skype: rpetryszak
> http://www.ebi.ac.uk/services/teams/expression-atlas



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From kclark at cshl.edu  Thu Oct 17 09:37:44 2013
From: kclark at cshl.edu (Youens-Clark, Ken)
Date: Thu, 17 Oct 2013 13:37:44 +0000
Subject: [Gramene] Can I submit data/maps to Gramene
In-Reply-To: <AAAPAGtjbGFya0Bjc2hsLmVkdQBGAAAAAABrSnULbvGDRbxFNcTRXntXBwD+/qSgQw+kTaKXf6NJjM0RAAAAESzQAACXfnwTyrgYRoEtgNLE+gIIAABOUjwPAAA=>
References: <AAAPAGtjbGFya0Bjc2hsLmVkdQBGAAAAAABrSnULbvGDRbxFNcTRXntXBwD+/qSgQw+kTaKXf6NJjM0RAAAAESzQAACXfnwTyrgYRoEtgNLE+gIIAABOUjwPAAA=>
Message-ID: <etPan.525fe829.4e6afb66.7d3e@capitan>

On October 17, 2013 at 7:13:41 AM, wangch16 (wangch16 at 126.com) wrote:
> Dear, 
> I have some allelic information about microsatellite, and want to submit these data to Gramene. How can I do?

I handled this.

Ken


