Rich,
You can convert base quality scores using the FASTQ Groomer tool. Note that
Galaxy tools typically work with Sanger (Phred+33) quality scores.
Good luck,
J.
On Aug 29, 2011, at 10:48 PM, Richard Mark White wrote:
> Hi,
> Thanks very much. I've tried this, but one thing I have noticed
Hello David,
The main hub for administration tasks is:
http://galaxyproject.org/Admin
To set up data, please see "Data Integration" and "NGS Local Setup".
If this is just your own local instance, you may not need to follow all
of the procedures. And you are correct, any log in would be specifi
Hi everybody,
I am developing the application on Galaxy server. One of the requirement is
to create user specific list of options. Is it possible to access somehow
$__user_email__ in tag or in ?. I did not found
documentation how to used cheetah in galaxy tool xml files but from files
provided
Hi,
I am learning how to install and configure Galaxy on our computer cluster. Many
third party tools, for example, bowtie, samtools, R and so on, have to be
installed and configured in order to install galaxy. Do I have to convert the
third party tools to MPI version in order to run the tools
Hi jen and galaxy users, when I try to use cufflinks in GALAXY and select "use
reference annotation", I am NOT sure how to get the annotation file in GTF
format for cufflinks.
I was trying to down-load the annotation file from Illumina donated package in
Cufflink website, I am NOT sure this is
>Sorry this is old but I tried recompiling torque after setting the
>NCONNECTS to 20 and the issue's still there.
>
>But there's more: It doesn't affect only flagstat but other non-linear
>workflows. One of the two jobs that are submitted when their "father"
>stopped running triggers the same error
If using Ensembl make sure it is properly formatted.
Vasu
--- On Tue, 8/30/11, Peng, Tao wrote:
From: Peng, Tao
Subject: [galaxy-user] annotation file for cufflinks
To: "Jennifer Jackson" , "galaxy-user"
Date: Tuesday, August 30, 2011, 1:52 PM
Hi jen and galaxy users, when I try to use cu
August 30, 2011 Galaxy Development News Brief
http://galaxyproject.org/wiki/News%20Briefs/2011_08_30
Source: http://getgalaxy.org
new: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist
upgrade: % hg pull -u -r 949e4f5fa03a
What's New
ISMB/ECCB, BOSC, and 3DSIG 2011 Slides
UCSC should work fine.
Vasu
--- On Tue, 8/30/11, Peng, Tao wrote:
From: Peng, Tao
Subject: RE: [galaxy-user] annotation file for cufflinks
To: "vasu punj" , "Jennifer Jackson" ,
"galaxy-user"
Date: Tuesday, August 30, 2011, 10:53 PM
Hi I have down-loaded UCSC HG19 annotation files from
In the cufflink site, they have annotation from ucsc,ncbi & ensemble. not sure
which one to download and then load into galaxy?
thanks,
Tao
Sent from my iPhone
On Aug 30, 2011, at 5:52 PM, "vasu punj" wrote:
> If using Ensembl make sure it is properly formatted.
> Vasu
>
> --- On Tue, 8/30/11
Hi I have down-loaded UCSC HG19 annotation files from Cufflinks; Should I just
load genes.GTF file (about 100 MB) to galaxy for cufflink analysis?
Thanks,
tao
-Original Message-
From: vasu punj [mailto:pu...@yahoo.com]
Sent: Tue 8/30/2011 5:52 PM
To: Jennifer Jackson; galaxy-user; Pen
Hi Jelle,
Thank you very much for your help !
Best!
Yan-Hui Li
At 2011-08-26 16:09:16,"Jelle Scholtalbers" wrote:
>Dear Yan-Hui Li,
>
>you have to make sure the output files (and location) are named by
>Galaxy. It isn't enough to just have the output files in the right
>output directory.
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