Also, do I have make all the reference files executable?
On Wed, Feb 13, 2013 at 6:39 AM, Sachit Adhikari <
sachit.techner...@gmail.com> wrote:
> I downloaded the entire directory of UCSC for the reference gnome of
> Tophat2. It turns out that the Tophat2 and Bowtie2 uses the same reference
> gno
I downloaded the entire directory of UCSC for the reference gnome of
Tophat2. It turns out that the Tophat2 and Bowtie2 uses the same reference
gnome. I found a directory: Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index
with the files:
genome.1.bt2 genome.2.bt2 genome.3.bt2 genome.4.bt2 genome.r
Cummerbund is available in the Galaxy toolshed for use in local or cloud
Galaxies:
http://toolshed.g2.bx.psu.edu/view/jjohnson/cummerbund
We haven't put it on our public server yet because there are testing and
compatibility challenges that need to be addressed.
Best,
J.
On Feb 11, 2013, at 7
Hi Jen
Thanks for your information, I'm using the public Galaxy main server and the
job is yellow.It was a good point, I put the large dataset as the second input,
I will wait if no success I will treat as you said.
Milad Bastami
PhD student of Medical Genetics
Department of Medical Genetics
Sh
Hello Milad,
I am not sure if you are using the public Galaxy Main server
(https://main.g2.bx.psu.edu) or your own local computer, or if the jobs
are yellow and running or still grey and in the waiting-to-run stage.
If using Galaxy Main, and if actually running (dataset is yellow), this
type
I have been using cufflinks on Galaxy Main. I have downloaded the files
generated but they do not correspond to the file names expected by cummeRbund.
For example:
cummeRbund expects 4 tracking files (e.g isoforms.fpkm_tracking) , 4 .diff
files (e.g isoform_exp.diff).
Here is a trimmed ver
On Tue, Feb 12, 2013 at 5:54 AM, Makis Ladoukakis
wrote:
> Dear users,
>
> Has anyone encountered this problem before? I wrote a shell script which
> among other things calls some R scripts like this..
>
> Rscript rscript_to_use.R
>
> When I run it via terminal it's fine plus I have verified Rscri
I'm trying to joint two large intervals (one with 800,000 intervals and the
other with about 350,000 intervals) using operates on intervals > join tool . I
have no idea how long it should takes normaly. Two days have past and it is
still runnig. Is there any limitation in file size for this tool
Dear users,
Has anyone encountered this problem before? I wrote a shell script which among
other things calls some R scripts like this..
Rscript rscript_to_use.R
When I run it via terminal it's fine plus I have verified Rscript works. But
when I upload my tool to Galaxy and try to run it I g
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