Does anyone knows a step-by-step pipeline to SNP calling on illumina
dataset?
From the alignment to the end
thanks
Francesco
--
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the
Hello,
I cannot run MACS on the local Galaxy. When I install MACS version 1.4.,
it gives error something like cannot find macs. When I install version
1.3.7.1 it gives error /line 34, in module from MACS.OptValidator
import opt_validate ImportError: No module named MACS.OptValidator/
I
Dear Galaxy users,
Does anyone know how to merge several FASTQ groomer files by using
Galaxy? If not, is there any other program that can achieve this? The size of
one FASTQ groomer file is around 1GB. Thank you!
Best regards,
Xiefan Fang, Ph.D.
Postdoctoral associate
Department of
On Tue, Oct 16, 2012 at 8:22 PM, Fang,Xiefan xiefanf...@ufl.edu wrote:
Dear Galaxy users,
Does anyone know how to merge several FASTQ groomer files by using
Galaxy? If not, is there any other program that can achieve this? The size
of one FASTQ groomer file is around 1GB. Thank you!
Hello Amit,
Are you using the public Main Galaxy instance at
http://main.g2.bx.psu.edu (usegalaxy.org) or another server specific to
your project?
If you are working with a project's Galaxy server, then you will need to
contact the administrator running that instance. It sounds as if you
Hello,
Thank you for sharing your history. The difference in FPKM values can be
explained by the use of the -N option (Perform quartile normalization:
Yes). Set this to No to avoid the variable per-run normalization.
This has also been discussed at seqanswers.com:
Hi list,
Is there a currently a known problem with the export to file function?
I'm trying to migrate some data from the public galaxy to a private one;
the export function worked well with a small (~100mb) dataset, but it has
not been working with larger datasets (2GB) and I get the error:
Hello,
Yes, this has not changed. The reference GTF given to Cuffdiff must
contain all of the transcripts of the inputs:
http://user.list.galaxyproject.org/cuffcompare-inputs-td4654384.html
Run this as you have done previously:
Hi Dave,
Yes, if your Galaxy instance is on the internet, for entire history
transfer, you can skip the curl download and just enter the URL from the
public Main Galaxy server into your Galaxy directly.
To load large data over 2G that is local (datasets, not history
archives), you can use
Dave,
There's likely something problematic about your history that causing problems.
Can you share with me the history that's generating the error? To do so, from
the history options menu -- Share/Publish -- Share with a User -- my email
address
Thanks,
J.
On Oct 17, 2012, at 6:58 PM,
Hello Everyone. Ctrl+C or Ctrl+D doesn't stop the Galaxy server. In local
machine, I need to close the terminal and restart the terminal again.
However, in server I integrated several tools, now I need to restart the
server to test it. I used ./run.sh --reload doesn't restart the server and
I
With a certain version of Python there's been an issue stopping Galaxy
using ctrl+C. You can use 'sh run.sh --daemon' to have the process run in
the background and then 'sh run.sh --stop-damemon' to stop it.
Hope this helps,
Enis
On Thu, Oct 18, 2012 at 4:12 PM, Sachit Adhikari
Thanks. Helped me!
On Thu, Oct 18, 2012 at 11:02 AM, Enis Afgan eaf...@emory.edu wrote:
With a certain version of Python there's been an issue stopping Galaxy
using ctrl+C. You can use 'sh run.sh --daemon' to have the process run in
the background and then 'sh run.sh --stop-damemon' to stop
13 matches
Mail list logo
