[Feedback] Site Feedback: genome mapping file between B73 RefGen_v2 and B73 RefGen_v3

[Marcela K. Monaco]

Sorry, message went unfinished...
Last just wanted to point out the assembly converter tool at
http://ensembl.gramene.org/tools.html which will allow you to convert
coordinates between the v2 and v3 assemblies.
Hope this helps!

Marcela


On Tue, Sep 30, 2014 at 6:17 PM, Monaco, Marcela <mmonaco at cshl.edu> wrote:

> Hi Julie,
>
> Unfortunately we do not have a file like the one with discontinued IDs
> generated for the 5a gene set.  If it helps, these are the differences
> between the v2 and v3 (filtered/coding) gene sets:
>
> • Over 2,100 FLcDNAs had longer alignments to v3 compared to v2 (300
> absent in v2). Some genes split in v2 could be rebuilt completely.
> • 5b FGS (39,656) => 5b+ (39,475 protein‐coding genes)
>
> RefGen_v3 Gene Models include:
> • 251 novel v3 models (new gene ids)
> • 213 improved models
>             – 204 one-to‐one updates
>             – 9 merge two RefGen_v2 models
>             – 10 received new gene ids
>
> A paper describing in more detail the V3 assembly and gene build is near
> submission.  FOr
>
>
> On Tue, Sep 30, 2014 at 3:45 PM, feedback at gramene.org<mailto:
> feedback at gramene.org> <feedback at gramene.org<mailto:feedback at gramene.org>>
> wrote:
> URL         : http://ensembl.gramene.org/Zea_mays/Info/Annotation/
>
> Subject     : Site Feedback: genome mapping file between B73 RefGen_v2 and
> B73 RefGen_v3
>
> Name        : Julie Leonard
>
> Email       : julie.leonard at syngenta.com<mailto:julie.leonard at syngenta.com
> >
>
> Organization: Syngenta
>
> Comments    :
>
> Hi.  I wanted to know if you have created a gene and/or transcript mapping
> file between B73 RefGen_v2 (5b.60) and B73 RefGen_v3 (AGPv3).  If so, is
> this available for the public.  I'm looking for something similar to this
> file:
> ftp://ftp.gramene.org/pub/gramene/maizesequence.org/release-5a/working-set/4a_discontinued_ids.txt
> .
>
> Thank you,
> Julie
>
> http://www.warelab.org/bugs/view.php?id=5042
>
>
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