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

[Marcela K. Monaco]

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 <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
>
> 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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