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 <james@jamestaylor.org <mailto:james@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 <jen@bx.psu.edu <mailto:jen@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-dev@bx.psu.edu <mailto:galaxy-dev@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_unin... > 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