Hi John,

If you have other sequence types, there are other alignment tool choices on the public Main server. The est2genome tool has a fairly specific use, so I thought that this was your input/goal.

For ChIP-seq, RNA-seq, or other NGS datatypes, please see the tools under 'NGS: Mapping' and 'NGS: RNA Analysis'. We have tutorials for these tools - from the top menu bar follow 'Shared Data -> Published Pages". Good places to start are 'Galaxy Exercises', 'Galaxy RNA-seq Analysis Exercise', and 'Using Galaxy' (but review the others as wanted, I am not sure what type of data you are working with). More tutorials are in our wiki here:
http://wiki.galaxyproject.org/Learn#Other_Tutorials

Other public Galaxy sites offer specialized tools for working with certain data types - the best way to find out what they have to is visit them and review. We keep a list of links in our wiki here:
http://wiki.galaxyproject.org/Big%20Picture/Choices ->
http://wiki.galaxyproject.org/PublicGalaxyServers

Good luck with your project! Next time, or if you have followup, please be sure to leave the mailing list in the cc to help us with tracking.

Thanks!

Jen
Galaxy team

On 2/4/13 8:08 AM, John Phillips wrote:
Are you sure that there is no way for me to align multiple sequences? I
apologize if I did not use the correct technical language, but from what
I understand, everyone seems to be citing you guys for sequence alignments.

Thank you,
-John


On Sun, Feb 3, 2013 at 1:34 PM, Jennifer Jackson <j...@bx.psu.edu
<mailto:j...@bx.psu.edu>> wrote:

    Hi John,

    The current link is:

    http://wiki.galaxyproject.org/__FTPUpload
    <http://wiki.galaxyproject.org/FTPUpload>

    We changed our wiki base and many of the older links do not
    redirect. I'll let our wiki admin Dave know about this and see what
    can be done. If this comes up again soon, the base always redirects
    to "http://galaxyproject.org -> http://wiki.galaxyproject.org"__,
    and clicking into "Learn" will likely take to you want to go - the
    primary hub page for user documentation - including the links in
    tutorials (plus the wiki side navigation bar with a few different
    search options).

    And is true that we do not offer large scale EST to genomic
    alignment on the public server. Galaxy choices such as
    BLAST+/Megablast are for use with a local or cloud Galaxy instance.

    When using a local instance, the tool wrapper can be obtained from
    the Tool Shed (http://toolshed.g2.bx.psu.edu__). A cloud ami would
    have these tools as part of the package. You can also check the Tool
    Shed for other options - more are added all the time.

    Local: http://getgalaxy.org
    Cloud: http://usegalaxy.org/cloud

    Hopefully this helps,

    Jen
    Galaxy team


    On 2/2/13 3:17 PM, John Phillips wrote:

          1.


             To Whom it May Concern:


        I am using the Galaxy interface, and according to the tutorial
        screencast, I should be able to upload my own reference genome. The
        address given in the tutorial
        (http://galaxyproject.org/__FTPUpload
        <http://galaxyproject.org/FTPUpload>) leads
        to a 404 file not found page. I was wondering if there is an
        alternative
        site that can allow me to do this.

        Also, I tried to use the est2genome tool in order to try and
        align my
        uploaded sequences. It would only allow me to compare two
        sequences at a
        time. Is it possible to align a larger number of sequences at
        once? I
        understand there are other programs that allow for this kind of
        procedure (e.g. Sequencher), but I would like to do this in Galaxy.

        Thank you for your time,

        --
        -John G. Phillips
        Graduate Research Assistant
        University of Tulsa
        231-233-6914 <tel:231-233-6914>


        _____________________________________________________________
        The Galaxy User list should be used for the discussion of
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        at usegalaxy.org <http://usegalaxy.org>.  Please keep all
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    --
    Jennifer Hillman-Jackson
    Galaxy Support and Training
    http://galaxyproject.org




--
-John G. Phillips
Graduate Research Assistant
University of Tulsa
231-233-6914

--
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org
___________________________________________________________
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/

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