[Feedback] Site Feedback: new barley 2H assembly

[Marcela K. Monaco]

Dear Shelly,

Sorry, I missed to enter the barley genome as update in our previous
release 43 and have just corrected the Genomes table in
http://gramene.org/release-notes-43

We has been recommended to us to advise users to stick to the contig
coordinates, and only project to chromosomal coordinates when absolutely
necessary.

Thank you,

Marcela

On Tue, Feb 3, 2015 at 2:46 AM, Shelly Hen Avivi <
shelly.hen-avivi at weizmann.ac.il> wrote:

> Dear Marcela,
>
> Thanks for your answer.
> I looked at the links you sent me, I don't see any genome update (I hope I
> do not miss anything). So- I still don't understand- if no update was done
> to the barley genome, how the genomic region now looks totally different?
> The genes are localized in very different locations from what used to be
> until recently. I just want to verify that this is on purpose and not a
> problem in the browser...
>
> Thanks, Shelly
>
> ~~~
> Shelly Hen- Avivi
> Asaph Aharoni’s Lab
> Dept. of Plant Sciences
> Weizmann Institute of Science
> Rehovot 76100
> Israel
> +972-8934-2275
> ________________________________
> From: mkmonaco.cshl at gmail.com [mkmonaco.cshl at gmail.com] on behalf of
> Marcela K. Monaco [mmonaco at cshl.edu]
> Sent: Monday, February 02, 2015 6:53 PM
> To: Shelly Hen Avivi; feedback at gramene.org
> Subject: Re: [Feedback] Site Feedback: new barley 2H assembly
>
> Dear Shelly,
>
> The last update performed on barley was the addition of the chloroplast
> genomes around Sept 2014, see http://www.gramene.org/release-notes-42.
>
> All the information that we have about the assembly and gene annotations
> for barley is available in the barley webpage, see
> http://ensembl.gramene.org/Hordeum_vulgare/Info/Annotation/#assembly
> (you get here by clicking on "More information and statistics" from
> http://ensembl.gramene.org/Hordeum_vulgare).
>
> Thanks,
>
> Marcela
>
> On Sun, Feb 1, 2015 at 5:28 AM, feedback at gramene.org<mailto:
> feedback at gramene.org> <feedback at gramene.org<mailto:feedback at gramene.org>>
> wrote:
> URL         : http://www.gramene.org/node/323
>
> Subject     : Site Feedback: new barley 2H assembly
>
> Name        : Shelly Hen- Avivi
>
> Email       : shellyha at weizmann.ac.il<mailto:shellyha at weizmann.ac.il>
>
> Organization: Weizmann institute of science
>
> Comments    :
>
> Hello,
>
> I find my barley genes of interest in a very different genomic region
> comparing to what I found previously. The genes are located in 2H
> chromosome.
> Have you updates the 2H assembly? Was is dramatically changed? Is the new
> assembly more reliable?
>
> Many thanks
> Shelly
>
> http://www.warelab.org/bugs/view.php?id=5112
>
>
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>
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