On Wed, Nov 6, 2013 at 12:08 PM, Fabrice Besnard
fbesn...@biologie.ens.fr wrote:
Would you have any advice to select the output format, or alternatively,
a tool in Galaxy that can convert pileup into .vcf?
Hi Fabrice,
I believe you only get the BCF output when Genotype Likelihood
Computation
On Tue, Sep 24, 2013 at 7:58 AM, Georgios Magklaras
georg...@biotek.uio.no wrote:
Hi,
Do you have best recipes for SFTP/Aspera upload gateway integration to
Galaxy? We would welcome advise on that matter.
Hi,
I haven't implemented yet, but I'm planning on using plain scp(windows
user can
Not the most convenient solution, but what I normally do in this situation
is to combine the two files, filter then split again. There are tools for
combining and splitting paired fastq files in Galaxy.
Hope it helps,
Carlos
On Jan 8, 2013 12:55 AM, 柴田 弘紀 hshib...@gen.kyushu-u.ac.jp wrote:
Hi
On Tue, Nov 6, 2012 at 2:27 PM, greg margeem...@gmail.com wrote:
Could anyone provide me with some basic directions on how to set it up
with virtualenv? I've never used it before.
I do this by adding this to the ~/.bashrc file of the user running
galaxy( in galaxy.fedora-init: RUN_AS=galaxy)
Hi Sachit,
Björn answer is correct. The issue is what is a tool. There are what
Galaxy calls tools. Some of which are installed by default and some
of which you can install from the toolshed. There are in many cases
just wrappers to third-party tools that need to be installed and
available in the
Hi Jianguang,
I'm the author of cummeRbund wrapper in the test Galaxy Tool Shed. I
never got around to quite finish it, that's why I never submitted to
main. Also cummeRbund received a big update since the time I was
writing this wrapper. I don't think I can recommend using the wrapper
in its
Hi Mathew,
Regarding 1 you might want to read this thread:
http://user.list.galaxyproject.org/Problem-with-Depth-of-Coverage-on-BAM-files-GATK-tools-td4654147.html
All tools from GATK are limited to hg_g1k_v37 as far as I know.
Best,
Carlos
On Mon, Aug 6, 2012 at 10:30 AM, Mathew Bunj
Also make sure you are using TABs to separate the fields in the .loc
file, this has bitten me several time in the past. My vim config
places 4 spaces instead of TAB, to deactivate this option you can do
:set noexpandtab.
Hope it helps,
Carlos
On Thu, Jul 5, 2012 at 4:39 AM, Avik Datta
Hi Lilach,
Sorry for the late response. Jen just confirmed the disadvantages of
my approach. I don't know how difficult could be for you to double
check the coordinates you have in your interval file are correct for
hg_g1k_v37. If you feel confident they will work and want to proceed,
you could
Hi Jennifer,
This is a subject I'm interested in. I wonder if you could share a
workflow to estimate percentage of reads mapping to for example
exomes(I can get the coordinates for a GFF dataset). I have a mapping
result for RNA-seq data and by looking in the browser, it seems to
also have a lot
Jiwen, I wonder if you are thinking about the situation where you
could be discarding reads that are to short after trimming?. In that
case you could be getting the two files out of sync. If this is the
case, I think you do need to join the files first, do the trimming and
then take them apart
Hi,
I need to sort a BAM file by read names, I was wondering if this is
possible with a tool included in Galaxy?
I know any BAM file produced inside Galaxy will be sorted by
coordinates, but I couldn't find an option to change this to queryname
in any tool. Picard has the tool SortSam[1],
Hi Jiwen,
This is a subject that has me very confused too. This thread at
seqanswer didn't help much either:
http://seqanswers.com/forums/showthread.php?t=8730
But it does have some good comments on the subject.
I did try using the two possible options I can think of:
fragment length - pair end
Hi Jen,
I have a related question. If Illumina 1.9 is already in Sanger
format, is it still necessary to groom the FASTQ files for TopHat?
Would it be enough to directly change the data type to Sanger without
grooming?
Thanks,
Carlos
On Wed, Feb 29, 2012 at 10:57 AM, Jennifer Jackson
Hi,
I ran into this error running cuffdiff. I had a hard time debugging
this user error, so I though it would be nice to share the solution.
This was in a local instance, but I don't see why it wouldn't happen
in Galaxy Main under the same circumstances.
Tool execution generated the following
was doing that.
In fact I want bam files (I'm also using GATK) so this is really helpful.
Cheers,
Clare
On Thu, Jan 19, 2012 at 2:32 AM, Carlos Borroto
carlos.borr...@gmail.com wrote:
Hi Clare,
I ran into a similar question testing out GATK pipeline on Galaxy. My
solution was to always
Hi,
I'm trying to test a workflow using tools only available on the test
server, for this I have uploaded a limited subset of my data that
should run fairly quickly. The first step is a BWA mapping, but the
job has being in the queue since yesterday. Is it fine to run this
kind of test there?
cluster was down yesterday for maintenance. Restarting the BWA job
should initiate the run.
Hopefully this helps,
Jen
Galaxy team
On 11/22/11 7:56 AM, Carlos Borroto wrote:
Hi,
I'm trying to test a workflow using tools only available on the test
server, for this I have uploaded a limited
.
The http: address can be found by by selecting properties on the disk
icon. Instead of downloading, you can just copy the http:.
I hope this helps,
Mike
--- On *Tue, 11/22/11, Carlos Borroto carlos.borr...@gmail.com* wrote:
From: Carlos Borroto carlos.borr...@gmail.com
Subject: Re
Hi,
I would like to run Unified Genotyper on a region of a BAM file, I
see the advance option A list of genomic intervals over which to
operate exist and seems to be what I need. The problem is I only get
a drop-down menu with the single option Selection is optional, which
I don't understand.
Hi Paul,
If you manage to get Xgrid working with galaxy, please share your
success, as I would love to try it.
But know that you can use SGE on Mac OS X. I was able to get it
working by following this blog post and screencast:
http://www.bioteam.net/2010/02/grid-engine-6-2-on-mac-os-x/
I tried
Hi,
The main Galaxy server is failing to schedule tophat's jobs. Giving error:
Unable to queue job for execution. Resubmitting the job may succeed.
I've been able to run other tools jobs.
Thanks,
Carlos
___
The Galaxy User list should be
This problem went away. Thanks.
On Tue, Aug 9, 2011 at 10:55 AM, Carlos Borroto
carlos.borr...@gmail.com wrote:
Hi,
The main Galaxy server is failing to schedule tophat's jobs. Giving error:
Unable to queue job for execution. Resubmitting the job may succeed.
I've been able to run other
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