Hello Stanislas,
To use a custom reference genome with Bowtie2/Tophat2, the genome needs
to be loaded using FTP into your history in .fasta format. UCSC is one
source, in the downloads area. It will require a download from there
first. http://genome.ucsc.edu or from our rsync server. Just be aware
that rat may be too large to run as a custom genome on the public server
with this tool (I haven't tried it). If the tool ends with a memory
error, then that is the problem.
http://wiki.galaxyproject.org/Support#Custom_reference_genome
http://wiki.galaxyproject.org/Support#Reference_genomes
http://wiki.galaxyproject.org/Admin/Data%20Integration#Get_the_data
We do have plans to add more indexes genomes for Bowtie2/Tophat2, but
the public server migration is the priority right now. There are
alternate wrappers available for Tophat (v1) in the Tool Shed (for
SOLiD), and also Tophat2, for use in a local, cloud, or slipstream
Galaxy. Our test server (https://test.galaxyproject.org/) has Tophat for
SOLiD loaded, but this server is where we really do test, and quotas are
small (10G) - so, tool problems are not supported and it is not
recommended unless for test/trial runs. Both tools have links to
documentation, with the Tophat2 website being a great resource to better
understand how the tools differ (along with the google support group).
I would estimate that more indexes will be available starting in about a
month, but it could be sooner/later.
Thanks!
Jen
Galaxy team
On 10/12/13 1:33 PM, Stanislas Werfel wrote:
Hi,
I am new to the field of RNA-Seq analysis. I'd be very greatful if
somene could help me with the following issue:
I'm using the Galaxy Main plattform and would like to run Tophat2 on
RNA-Seq data from rat. However in Main under Tophat2 there are only
built-in human and mouse genomes, while a lot more genomes are
vailable under Tophat for Illumina.
I tried to import the rat genome sequence using the built-in UCSC
Table browser, however I only managed to get a full genome as one
FASTA file with all the different sequences. After mapping to this
genome I can't see any hits when I click "display at UCSC main" on
accepted hits. So I assume that the mapped reads do not conform to the
official reference rat genome (rn5).
So how can one solve this isse?
-Is there a way to import a proper genome for use with Tophat2?
Ideally directly indo Galaxy without prior download.
-If not, how does Tophat2 differ from "Tophat for Illumina". Can one
also analyze non-Illumina data with that? As I understand it Tophat2
is faster than the previous version?
Thanks in advance for any help.
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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:
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please use the interface at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
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