Re: [galaxy-user] Tophat etc
I actually have a very basic question on the topic of Cufflinks since
I'm a bioinformatics neophyte...
I have performed a BWA alignment of Illumina RNA-seq data to the
appropriate annotated cDNA database... so it's currently in SAM
format.
Can I get this data in a form that can be processed by Cufflinks using
the tools available on Galaxy or not? So far I haven't been able to
figure this out.
I assume that Cufflinks is the only (best?) way to look at transcript
abundance on Galaxy?
Thanks for any help!
David Coil, PhD
UC Davis Genome Center
On Wed, Nov 3, 2010 at 6:17 AM, Jeremy Goecks <jeremy.goecks(a)emory.edu> wrote:
> Can you tell me which version of Tophat
v1.0.14
In the next couple weeks we'll update to the newest version, v1.1.2
> and Cufflinks is being used
The most recent version, v0.9.2
> and whether the Tophat you have uses a GFF or GTF file to help it find splices (this
is an option I believe)?
Not currently, but we'll add this features in the next couple weeks.
Best,
J.
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