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
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.
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.
On 10/12/13 1:33 PM, Stanislas Werfel wrote:
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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