Hello Somayyeh,

These data are from the same authors/release build. At Ensembl, the same 5 core chromosomes plus an additional 78 unplaced scaffolds are available. The data authors decided not to include these scaffolds in their publication at NCBI.


For a primary genome, I suggest that we use the core 5 chromosomes as this is what was published externally to NCBI by the authors. Would this also be your preference? Both options are possible. Many genomes have unmapped scaffolds included in the Galaxy genome builds, however they are usually published at NCBI if/when the genome is submitted there.

Thank you!

Jennifer


On 7/21/11 5:41 AM, Somayyeh Fahiminiya wrote:
Hi Jen,


Thanks for your email and sorry to be late .

Please look at :
wget
ftp://ftp.ensemblgenomes.org/pub/plants/current/fasta/brachypodium_distachyon/dna/Brachypodium_distachyon.Brachy1.0.dna.toplevel.fa.gz

I dont know if it is more recent or  the same version as yours



Thanks again

somayyeh




On Mon, Jul 11, 2011 at 9:05 PM, Jennifer Jackson <j...@bx.psu.edu
<mailto:j...@bx.psu.edu>> wrote:

    Hello,

    To confirm: the correct source would be this project, only has
    chromosomes 1-5, at NCBI? Or is there a preferred (more
    complete/recent) source?

    http://www.ncbi.nlm.nih.gov/__bioproject/32607
    <http://www.ncbi.nlm.nih.gov/bioproject/32607>

    Once we have the source confirmed, we can add this genome to our
    to-add list,

    Best,

    Jen
    Galaxy team


    On 7/7/11 6:25 AM, Somayyeh Fahiminiya wrote:

        Hello everyone,

        Could you plz add the genome of "*Brachypodium distachyon*" to
        the Galaxy.

        Thanks in advance



        _____________________________________________________________
        Please keep all replies on the list by using "reply all"
        in your mail client.  To manage your subscriptions to this
        and other Galaxy lists, please use the interface at:

        http://lists.bx.psu.edu/


    --
    Jennifer Jackson
    http://usegalaxy.org/
    http://galaxyproject.org/



--
Jennifer Jackson
http://usegalaxy.org/
http://galaxyproject.org/
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

 http://lists.bx.psu.edu/

Reply via email to