Hi Pengfei,

The "User -> Custom Builds:" form is used to set up genomes for use with Trackster. To use custom reference genomes with tools from the left tool panel, only the fasta dataset in the history is needed. It sounds like you already have loaded this, but if not, do this before following the steps below, using FTP to load if the genome is large: http://wiki.g2.bx.psu.edu/FTPUpload


These are the steps to extract sequences with a custom genome:

1 - starting with the tool "Fetch Sequences -> Extract Genomic DNA"
2 - set "Fetch sequences for intervals in:" to be the BED file of coordinates
3 - set "Source for Genomic Data:" to be "History"
4 - the form will refresh to reveal a new menu option, set "Using reference file:" to be the dataset from your history that is the fasta version of your reference genome
5 - set "Output data type:" to be "FASTA"

It is important that the chromosome/scaffold names in the BED file are identical to the identifiers in the FASTA reference genome dataset. If there are mismatches, an error will result and corrections to the IDs should be made.

Hopefully this helps, but if you continue to have problems, please send in a bug report (using the green bug icon) from the red failed Extract job and we can provide feedback.

Best,

Jen
Galaxy team

On 2/17/12 8:25 AM, Pengfei Yu wrote:
Hi Jeremy,

Thanks for the help! I can upload fasta data for custom builds
(name:'NCI-H209-hg18'; key:'NCI-H209-V1') now. but when I try to use a
bed file specific for this custom builds to fetch sequences from this
custom genome, it gives error information that no sequences are
available for 'NCI-H209-v1'.
I might do something wrong, do you know what would be the reason?

Thanks!
Pengfei

On Fri, Feb 17, 2012 at 7:40 AM, Jeremy Goecks <jeremy.goe...@emory.edu
<mailto:jeremy.goe...@emory.edu>> wrote:

    Hi Pengfei and Noa,

    I suspect this was a temporary problem related to software issues
    that we encountered yesterday. Please try again and let us know if
    you're still having problems.

    Also, note that either a FASTA dataset or a Len file is needed, but
    not both. Using a FASTA dataset enables viewing genome data in
    Trackster.

    Best,
    J.


    On Feb 17, 2012, at 12:00 AM, Noa Sher wrote:

    I also had exactly the same problem yesterday - glad to see that
    maybe it wasn't just me.
    Happy for help!
    Noa

    On 16/02/2012 22:24, Pengfei Yu wrote:
    Dear sir or madam,

    I am using galaxy public server and I am trying to build a custom
    genome using the function "custom Builds" in "user" section.
    I specified the Name, Key and uploaded the genome fasta file also
    the chromosome length file. But when I click "submit", galaxy
    gave an error information like that:
    ""
    *Server Error:*
    An error occurred. See the error logs for more information. (Turn
    debug on to display exception reports here)
    ""
    I don't know where to find the error logs and how to turn debug
    on. Could you tell me how to fix the problem and upload the
    custom builds?
    Thanks a lot!

    Pengfei
    --
    Pengfei Yu
    Center of Biophysics and Computational Biology
    University of Illinois Urbana-Champaign
    Illinois, 61820, US
    Cell phone:217-898-6301 <tel:217-898-6301>



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--
Pengfei Yu
Center of Biophysics and Computational Biology
University of Illinois Urbana-Champaign
Illinois, 61820, US
Cell phone: 217-898-6301



___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

   http://lists.bx.psu.edu/listinfo/galaxy-dev

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/wiki/Support
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

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