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
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.

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:


To manage your subscriptions to this and other Galaxy lists,
please use the interface at:


To search Galaxy mailing lists use the unified search at:


Reply via email to