Hi Sandra,
Galaxy can certainly be used to correlate a set of unknown genomic
coordinates with another annotated set of genomic corrdinates, such as
those available from UCSC, Biomart, etc.
The tool set to look at is Operate on genomic intervals and an example
of how these tools are used,
Hi Michael, sorry it took a while but we've figured out the root cause
of this issue and will be deploying a fix shortly. Thanks!
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Fri, Mar 22, 2013 at 4:20 PM, Michael Axtell mj...@psu.edu wrote:
Hi everyone.
I'm having an
Hi All,
Is there a size limit of dataset for running Tophat at Galaxy? If there is, how
many reads is the limit?
Thanks.
Jianguang
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the
Hi All,
When I tried to download the filtered datasets from my History at Galaxy to
my computer, I always got this error information:
Internal Server Error
Galaxy was unable to sucessfully complete your request
An error occurred.
This may be an intermittent problem due to load or other
James, great! Glad you isolated the bug and will fix. It will come
in handy for us (and maybe others).
Mike
On Wed, Mar 27, 2013 at 2:07 PM, James Taylor ja...@jamestaylor.org wrote:
Hi Michael, sorry it took a while but we've figured out the root cause
of this issue and will be deploying a
Hi Jianguang,
The limit for Tophat will most likely not be the number of reads, but
the total processing time when using the public Galaxy instance.
Currently, a job has 72 hours to complete, assuming that there is not a
memory problem before that time limit is reached.
But, there are some
Hello Els,
Have you seen the tool BEDTools - Create a BedGraph of genome
coverage? This would give you the coverage numbers, then you could
perform statistics on those numbers.
You could also Convert from BAM to BED (there is an option to split
for spliced alignments) and if you had a bed
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