[Feedback] Site Feedback: linke to balrey genome sequence

[Dan Bolser]

sm = soft masked (i.e. repeats in lower case).

He may be looking at the 'genome' file, which is a mix of all 'toplevel'
sequence. i.e. you can point him here:
ftp://ftp.ensemblgenomes.org/pub/plants/release-25/fasta/hordeum_vulgare/dna/README


Cheers,
Dan.

On 10 March 2015 at 20:13, Marcela K. Monaco <mmonaco at cshl.edu> wrote:

> Hi Dan,
>
> About the assembly data for barley, I understand that this is more like a
> gene-ome and not a true assembly...  But why is the user refering to
> contigs?  I see a single pseudomolecule per file (with lost of Ns
> nonetheless)...
>
> Also rm = repeat masked, and sm = ?
>
> Thanks,
>
> Marcela
>
> ---------- Forwarded message ----------
> From: feedback at gramene.org <feedback at gramene.org>
> Date: Tue, Mar 10, 2015 at 3:36 PM
> Subject: [Feedback] Site Feedback: linke to balrey genome sequence
> To: "feedback at gramene.org" <feedback at gramene.org>
> Cc: "Steve Larson [USDA ARS]" <Steve.Larson at ars.usda.gov>
>
>
> URL         : http://ensembl.gramene.org/Hordeum_vulgare/Info/Index
>
> Subject     : Site Feedback: linke to balrey genome sequence
>
> Name        : Steve Larson
>
> Email       : Steve.Larson at ars.usda.gov
>
> Organization: USDA ARS
>
> Comments    :
>
> I think the link to the barley genome sequence assembly
> (File:Hordeum_vulgare.082214v1.25.dna.genome.fa.gz)
>
> at
>
> Index of
> ftp://ftp.ensemblgenomes.org/pub/plants/release-25/fasta/hordeum_vulgare/dna/
>
> is incorrect. This believe this file should contain about 20
> psuedomolecules, not 10,000 contigs
>
>
>
> http://www.warelab.org/bugs/view.php?id=5129
>
>
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>
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