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.
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
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.
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
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
James Taylor, Associate Professor, Biology/CS, Emory University
On Wed, Oct 16, 2013 at 3:31 PM, Jennifer Jackson <j...@bx.psu.edu
> 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
> listed (we really do test here). Also, the quotas are very small
> you want to use this tool, a local, cloud, or slipstream Galaxy is
> recommended. Full choices with details are listed here:
> 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,
> created. You can rsync the genome, but most genomes will not
have loc file
> entries and indexes for SOLiD already created - see the Tophat
> the command to create these:
> Hopefully this helps!
> 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
>> 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
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