Hi Loyal,
Thanks alot for your great tool, Cummerbund. I have used "tuxedo suit"
tools for analyzing my RNA-seq data. I was wondering if there is any
facility in Cummerbund to visualize the isoforms and splicing events. For
example: for each gene showing us different exons and introns
in known isoforms as well as novel isoforms. Thanks

Sincerely Yours,
Delasa Aghamirzaie
Genetics, Bioinformatics, and Computational Biology (GBCB) PhD Student
Virginia Tech
Blacksburg, Virginia



On Fri, Jun 21, 2013 at 10:13 AM, Himanshu Sharma <
hsharm03@students.poly.edu> wrote:

> Thanks a lot Loyal,
> I am trying to do a comparison of drug treatment on various resistant and
> sensitive tumors. I will think about how I can design the cuffdiff analysis
> to merge them all together.
> I really appreciate your effort to reply back.
> Thanks,
> Himanshu
> ________________________________________
> From: Loyal A. Goff [lgoff@csail.mit.edu]
> Sent: Friday, June 21, 2013 10:05 AM
> To: Himanshu Sharma
> Cc: bioconductor@r-project.org
> Subject: Re: [BioC] CummeRbund multiple cases
>
> Hi Himansu,
> It is certainly possible to have 2-3 different concurrent connections to
> the different SQLite databases that would allow you to interact with all of
> the data points in the same session, but at this point, there is no
> seamless way to 'integrate' the results of multiple cuffdiff runs.  This is
> by design however as each cuffdiff run does its own model fitting and
> normalization that allows samples within a run to be directly comparable.
>  Depending on what it is you are trying to do, the best solution may be to
> create a new cuffdiff analysis that incorporates all samples across all
> analyses.  Please let me know if I can be of any more specific help.
>
> Cheers,
> Loyal
>
>
>
>
> On Jun 20, 2013, at 1:32 PM, Himanshu Sharma <hsharm03@students.poly.edu>
> wrote:
>
> > Dear Community,
> > I have my RNA-seq Differential expression results from Cuffdiff. I would
> like to make some plots and figures using CummeRbund. I have been using it
> for quite sometime and find it really good. I wanted to ask if I could
> combine 2-3 different analyses and merge the results in Cummerbund?.
> > Thanks,
> > Himanshu
> >
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> >
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