Hello:
I am a Galaxy-naive molecular, developmental biologist studying
repression/derepression of early embryonic gene expression in zebrafish
embryos.
After attending the Galaxy meeting I returned home and worked up two
mRNAseq files to determine RNA expression differences using cuffdiff
between
How does one get gene names when using cuffdiff when looking at gene
differential expression testing results?
I am doing some +/- exposure studies with zebrafish embryos and then
processing the 50bp single-ended fastq files through Galaxy with particular
interest in the cuffdiff readout of
Hello, I would like to download some GEO files that complement my own
research with zebrafish embryos but apparently GEO is now only providing
.sra flles.
For a not very experienced unix person, does Galaxy have a tool for this or
is there a clear description somewhere else of how to do it for
Problem:
when downloading steps in histories back to my computer the files are
sometimes incomplete (by incomplete I mean a significantly smaller size
that given during the download indicator)
Description:
after processing RNAseq files on main Galaxy I have the memory to download
steps or
in.
Sincerely,
Elwood Linney
Professor of Molecular Genetics and Microbiology
Duke University Medical Center
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connect with Galaxy online to transfer data.
Is this a problem that can be solved-either at my end or at Galaxy?
Elwood Linney
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these on the cloud
so its hard to estimate setup costs and specific requirements.
Elwood Linney
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Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all
Hello, I have been waiting a few weeks to process some RNA seq datasets
but woke up this morning with lots of steps red. I thought it just might
be because of the movement of the system but I processed steps for some
histories and everything has turned red.
I also noticed that online Galaxy now
if this is just some interface problem with a different
version of the software that was included with the move, or a reference
genome that does not interface with Cuffdiff. It has happened with about 5
different histories.
Is anyone else having this problem? And found a solution?
Elwood Linney
Hello,
I am sure this has come up before and maybe I missed the answer.
If in using cuffdiff I run a sample 1(3 repeats) vs a sample 2 and then
run the same sample 1(3 repeats) against a sample 3 or a sample 4, I get
different value for fpkm from sample 1 each time.
Is there something going
Can you add danrer7 as a reference genome for tophat2 for online Galaxy?
Its there for tophat for Illumina.
Elwood Linney
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