Anne:
1. This question is more appropriate for galaxy-user list, so I'm forwarding
this e-mail.
2. When you map reads against a reference these initial dataset is your raw
reads (or perhaps I do not fully understand your question).
Thanks!
anton
galaxy team
On Mar 16, 2011, at 10:58 AM, Ann
mail client. For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
>
> http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> To manage your subscriptions to this and other Galaxy lists,
> please use the int
e the "saved histories" is empty. I still have everything
> open at my home computer. Do you think I still can save it there?
>
> Thanks a lot again for your help,
>
> Tania
> From: Anton Nekrutenko [mailto:an...@bx.psu.edu]
> Sent: Thursday, March 24, 2011
Galaxy source code, please
> use the Galaxy Development list:
>
> http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
> htt
). With 30 mil reads
this will likely take some time though.
Thanks,
anton
On Mar 29, 2011, at 11:38 AM, Surya Saha wrote:
> These are Illumina reads
>
> -S.
>
> On Tue, Mar 29, 2011 at 11:37 AM, Anton Nekrutenko wrote:
> Are these illumina or solid reads?
>
> Tx,
>
In a hacky way, where you translate "/1" into something else such as two spaces
" ", or your favorite chemical element such as "He" ;)
a.
On Mar 29, 2011, at 4:00 PM, Surya Saha wrote:
> The sequence names do end in /1 and /2 but that can be fixed using Manipu
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
Anton Nekrutenko
http://nekrut.bx.psu.edu
http://usegalaxy.org
___
The Galaxy User list should be used for the discussion
instances and the Galaxy source code, please
> use the Galaxy Development list:
>
> http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
> http://lists.bx.psu.edu/
Anton Nekrutenk
scriptions to this and other Galaxy lists,
> please use the interface at:
>
> http://lists.bx.psu.edu/
Anton Nekrutenko
http://nekrut.bx.psu.edu
http://usegalaxy.org
___
The Galaxy User list should be used for the discussion of
Galax
informatician
> come over and help me on Thursday and I think your tips will be of help.
> My only problem with Galaxy is that I have to keep on clearing my cache in
> order to get the history to display correctly, is there another way of
> solving this issue?
>
> Best rega
y clarification in this area would also be much
> appreciated. Again, time is money!
> I hope this helps many of us!
>
> Unfortunatly, I will not be in Pitt to ask these questions in person.
>
> Thanks in advance!!!
>
> Mike
>
> --- On Tue, 4/5/11, Lali wrote:
>
&g
105 0 0 0 105
> chr1 103461507 103461508 T A 255 255 60
> 87 82 0 0 0 82
> chr1 104166495 104166496 T C 255 255 60
> 168 0 157 0 5
t; http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
> http://lists.bx.psu.edu/
Anton Nekrutenko
http://nekrut.bx.psu.edu
http://usegalaxy.org
__
discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org. Please keep all replies on the list by
> using "reply all" in your mail client. For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
r discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
>
> http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
> http://l
g. Please, check that your input
csfasta and QUAL files have exactly the same number of non-comment lines.
Thanks for using Galaxy,
anton
galaxy team
PS Your _R3 files are fine.
Anton Nekrutenko
http://nekrut.bx.psu.edu
http://usegalaxy.org
On May 26, 2011, at 10:50 AM, Jia-Xing Yue wrote:
&
Joanne:
Look under "NGS: QC and manipulation".
Thanks,
anton
Anton Nekrutenko
http://nekrut.bx.psu.edu
http://usegalaxy.org
On Jun 10, 2011, at 1:10 PM, Joanne Rampersad wrote:
Hi
Is there an stand alone ( ie not a component of Bowtie etc ) program
in galaxy that can filter or
Keith:
For large files use FTP upload as described here:
https://bitbucket.org/galaxy/galaxy-central/wiki/UploadViaFTP
Thanks for using galaxy,
anton
galaxy team
Anton Nekrutenko
http://nekrut.bx.psu.edu
http://usegalaxy.org
On Jun 11, 2011, at 6:50 PM, Keith Giles wrote:
> I converte
or using Galaxy,
anton
galaxy team
Anton Nekrutenko
http://nekrut.bx.psu.edu
http://usegalaxy.org
On Jun 22, 2011, at 4:15 PM, Joanne Rampersad wrote:
> Hi
> I have a few questions
>
> 1. I am trying to use Bowtie to map my data using a reference genome.
> the genome is avail
Dear Rad:
We do not yet have all necessary tools for making up such as workflow.
Thanks for using Galaxy,
anton
galaxy team
Anton Nekrutenko
http://nekrut.bx.psu.edu
http://usegalaxy.org
On Jun 7, 2011, at 12:07 PM, Radhouane Aniba wrote:
> Hi Galaxy users,
>
> I am new to Gal
end of Summer.
Thanks for using Galaxy,
anton
galaxy team
Anton Nekrutenko
http://nekrut.bx.psu.edu
http://usegalaxy.org
On May 18, 2011, at 7:39 PM, Andrea Edwards wrote:
> Hello
>
> I was wondering if there was anything available within galaxy that would let
> you do the fo
Kevin:
Is this a diploid or haploid organism?
anton
galaxy team
Anton Nekrutenko
http://nekrut.bx.psu.edu
http://usegalaxy.org
On Jul 12, 2011, at 11:38 PM, Kevin Pawlik PhD wrote:
> After viewing tutorials and reading the information associated with various
> tools, I ask that you
. However, piplines for proper (1000genomes-like) varinat calling that
include realignment and recalibration steps are coming by the end of the Summer.
Thanks!
anton
Anton Nekrutenko
http://nekrut.bx.psu.edu
http://usegalaxy.org
On Jul 13, 2011, at 1:43 PM, Kevin Pawlik PhD wrote:
>
Qiang:
I'm reposting this question to the galaxy-user mailing list.
Thanks!
anton
> Dear Anton,
>
> I am a PhD student in the Matrin-Luther University Halle-Wittenberg focused
> on honey bee Ecology.
>
> Galaxy is a very flexible tool to do RNA Seq analysis. I have a problem and
> need your
Diana:
It is best to direct such requests to galaxy-u...@bx.psu.edu mailing list,
which I am doing. Adding this genome should be possible, but will take us some
time.
Thanks,
anton
Anton Nekrutenko
http://galaxyproject.org
On Sep 12, 2011, at 1:23 PM, Diana Cox-Foster wrote:
>
Also, test instance (http://test.g2.bx.psu.edu) has TMap mapper, which was
recently rolled out for testing. The wrapper was contributed by Nils Homer. At
this time there are only E. coli indices, but more can be added.
a.
Anton Nekrutenko
http://galaxyproject.org
On Sep 28, 2011, at 10:18
Jessica:
No, dindel is not yet a part of Penn State Galaxy Instance.
anton
Anton Nekrutenko
http://galaxyproject.org
On Sep 28, 2011, at 12:21 PM, Golbus, Jessica wrote:
> Hi-
>
> I am using Galaxy for Indel analysis. Does the Indels from Sam analysis use
> Dindel to pu
Casey:
Not really except by making a screenshot.
Tx,
anton
Anton Nekrutenko
http://nekrut.bx.psu.edu
http://usegalaxy.org
On Oct 20, 2011, at 3:15 PM, Casey Bergman wrote:
> Dear Galaxy Team -
>
> [Apologies if this has been answered before on this list before...I couldn&
David:
>
> Question I: what are the small letters and what are the capitals here?
> Are these already masked, exons/introns or what?
> (I downloaded some of these sequences and repeatmasked myself. My pasked
> sequences overlap with some of "yours" written in small letters.)
>
In case of mouse
Boaz:
Try http://usegalaxy.org/galaxy101
Thanks,
anton
Anton Nekrutenko
http://nekrut.bx.psu.edu
http://usegalaxy.org
On Oct 21, 2011, at 12:45 PM, Boaz iga wrote:
> Hi Folks,
>
> I am just beginning to use galaxy and was wondering whether besides the
> tutorial video the
Hong:
I'm forwarding this to our official user mailing list. Please, use it in the
future for your inquiries.
Thanks!
anton
Anton Nekrutenko
http://nekrut.bx.psu.edu
http://usegalaxy.org
On Apr 3, 2012, at 4:37 PM, xu hong wrote:
> Hi Anton,
>
> I'm a biological s
ranges (such as
(ChrX:144,000,000-146,500,000)).
Thanks!
anton
Anton Nekrutenko
http://nekrut.bx.psu.edu
http://usegalaxy.org
On Apr 19, 2012, at 12:53 PM, Binnaz Yalcin wrote:
> Dear Anton,
>
> Can I do an anrichment analysis in Galaxy? if so, how?
>
> I want to know whet
Hi:
Alternatively you can note the SRA sequence identified and use Galaxy's EBI-SRA
datasource to import data directly.
a.
Anton Nekrutenko
http://www.galaxyproject.org
On Jan 31, 2013, at 8:58 AM, Björn Grüning wrote:
> Hi,
>
> you can try to import your SRA directly as fast
will now recognize you dataset.
Thanks and sorry for late reply.
anton
Anton Nekrutenko
http://www.galaxyproject.org
On Feb 22, 2013, at 3:58 AM, Andrew South wrote:
> NGS: SAM Tools
>
> I have generated a simple 6 column pileup from my BAM file but when I try to
> use the Filter Pileu
Justin:
Can you share a history with me via a link (click gear on the top rigt, choose
"share or publish" and click "Make history accessible via a link"; then e-mail
this link to me). I'll see what is happening.
Tx,
a.
Anton Nekrutenko
http://www.galaxyproject.org
Lilach:
This tool works on unaligned reads in fastq format before they are mapped.
It is useful for merging mates together into a single read for QC
processing, filtering, and trimming.
Thanks!
anton
On Wed, Sep 11, 2013 at 4:34 AM, lilach noy wrote:
> Hi all,
>
> Has anyone used FASTQ joine
hat it takes
> a few weeks to get a repy from that)?
>
> Elwood Linney
> Professor of Molecular Genetics and Microbiology
> Duke University Medical Center
>
--
Anton Nekrutenko
Associate Professor
Dept. of Biochemistry and Molecular Biology
www.galaxyproject.org
(814) 826-3051
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