g wrong".
Sincerely, but naively,
Elwood Linney
Professor of Molecular Genetics and Microbiology
Duke University Medical Center
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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 diffe
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 so
/bowtie_index/danRer7
/galaxy/main_pool/pool7/files/006/143/dataset_6143636.dat Exception in
thread Thread-1: Traceback (most recent call last): File
"/usr/global/python/2.6.5/lib/python2.6/threading.py", l*
Sincerely,
Elwood Linney
Duke University Medi
when I try to process groomed datasets through
Tophat and "Use a built-in genome" as reference it does not allow me an
option for the reference genome AND if I try to use a reference genome from
the UCSC download, it won't allow that.
So right now I am stymied--any advice?
Elw
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 compl
e new data just came 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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ese on the cloud
so its hard to estimate setup costs and specific requirements.
Elwood Linney
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at usegalaxy.org. Pleas
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
case there is
some kind of mismatch in the processing.
Before I remove them all and start them all over, I would appreciate
knowing if anyone else has identified where the block is.
Elwood Linney
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fdiff. This worked in
the past but my history are just getting thru Tophat or Cuffmerge and
stalling. Should I be doing this in a different manner?
This has been my second time around with these datasets after it was
suggested that I delete and start all over again.
Elwood L
know 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?
at a conference over next several days, so let's use galaxy-bugs as
> a cc whenever we communicate so nothing is left lingering, plus I know Nate
> was looking into some of your data. Jeremy may jump also in at any time and
> help - he is the author of the wrapper.
> >
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 wron
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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