Hello Lei,

These can go in the "bowtie_indices_color.loc" file. In fact, you don't need the "tophat_indexes" file as far as I know, those lines can be merged with what is in "bowtie_indexes". Both Bowtie and Tophat use the same indexes - one set for regular, one set for color. Then, both Bowtie2 and Tophat2 use the same indexes - only one type, no option for color. This structure is explained in more detail in the data link I sent and you can see examples in our rsync server's location files.


Jeremy/James - please correct me if I have any of this incorrect for their particular install. The above are the standard config instructions.

Thanks!
Jen
Galaxy team



On 10/16/13 12:54 PM, Lei Yan wrote:
Hi Jen and James,

Thanks for your info.
Yes, we are already running a cloud instance (http://galaxyclass.genenetwork.org/).
So if I can build the index for colorspace, then how to configure it?
And I didn’t find the “tophat_indexes_color” record in the Admin - “View data tables registry”. Please see attachment.


Lei Yan
Center for Integrative and Translational Genomics
The University of Tennessee Health Science Center


On Wed, Oct 16, 2013 at 2:35 PM, James Taylor <ja...@jamestaylor.org <mailto:ja...@jamestaylor.org>> wrote:

    They are already running a local instance.

    I didn't realize that bowtie required a different index for colorspace
    alignment. So Lei, you will have to build the index using bowtie-build
    -C.

    --
    James Taylor, Associate Professor, Biology/CS, Emory University


    On Wed, Oct 16, 2013 at 3:31 PM, Jennifer Jackson <j...@bx.psu.edu
    <mailto:j...@bx.psu.edu>> wrote:
    > Hello Lei,
    >
    > If genomes are not listed, that means that they are not indexed
    for use with
    > the tool. The test server is primarily for demonstration or test use
    > besides, and there could be other unexpected issues even if
    genomes are
    > listed (we really do test here). Also, the quotas are very small
    (10G). If
    > you want to use this tool, a local, cloud, or slipstream Galaxy is
    > recommended. Full choices with details are listed here:
    > http://wiki.galaxyproject.org/BigPicture/Choices
    > http://usegalaxy.org/toolshed
    >
    > Help for setup is here, with the galaxy-...@bx.psu.edu
    <mailto:galaxy-...@bx.psu.edu> mailing list
    > available for further support. Tools will need to be installed,
    and indexes
    > created. You can rsync the genome, but most genomes will not
    have loc file
    > entries and indexes for SOLiD already created - see the Tophat
    manual for
    > the command to create these:
    >
    
http://wiki.galaxyproject.org/Tool%20Shed#Installing.2C_maintaining_and_uninstalling_tool_shed_repositories_within_a_Galaxy_instance
    > http://wiki.galaxyproject.org/Admin/Data%20Integration
    > http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup
    >
    > Hopefully this helps!
    >
    > Jen
    > Galaxy team
    >
    >
    > On 10/16/13 11:57 AM, Lei Yan wrote:
    >>
    >> Hi all,
    >>
    >> We are trying to use “Tophat for SOLiD”.
    >> But this tool (Tophat for SOLiD) does not seem to be linked to the
    >> reference genomes that are installed. I can see those genomes
    on the Tophat
    >> for illumina tool and the other tools that require a reference
    genome.
    >> Please see attachments.
    >> Does anybody have any ideas for this? Thanks a lot.
    >>
    >>
    >> Lei Yan
    >> Center for Integrative and Translational Genomics
    >> The University of Tennessee Health Science Center
    >
    >
    > --
    > Jennifer Hillman-Jackson
    > http://galaxyproject.org
    >



--
Jennifer Hillman-Jackson
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Reply via email to