[Gramene] Fwd: Re: collaboration with ATLAS on sharing plant data on ensembl browser (Attn: Paul Kersey and Doreen)
Robert Petryszak
rpetry at ebi.ac.uk
Thu Oct 17 06:50:37 EDT 2013
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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