Original Message
Subject: Re: [galaxy-user] error occurred when converting the SOLID output
to fastq
From:"Jia-Xing Yue"
Date:Wed, June 8, 2011 5:48 pm
To: "A
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:
Tanita:
Click "Options" at the top of the history pane and choose "Saved histories".
You will see your old history listed in the middle pane.
Thanks,
anton
galaxy team
On Mar 24, 2011, at 12:15 PM, Fuchs, Tania wrote:
> Hello,
>
> I worked on my home compute
Tanita:
Histories are saved automatically, but you need to be logged in to your Galaxy
account.
Thanks,
anton
On Mar 24, 2011, at 3:13 PM, Fuchs, Tania wrote:
> Hi Anton,
>
> Thanks for the tip. I did not save my history, so I guess it was not saved
> automatically, sinc
Are these illumina or solid reads?
Tx,
anton
On Mar 29, 2011, at 11:29 AM, Surya Saha wrote:
> Hi,
>
> I have two fastq files with the forward(/1) and reverse(/2) paired reads. The
> reads are not in same order in either file, some pairs are absent/missing and
> the file
). 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
trial-strength" diploid genotyping
functionality in Galaxy in the next two-three months that will include more
sophisticated genotypers, recalibration and realignment tools, and novel
visualization approaches.
Thank for using Galaxy.
anton
galaxy team
On Apr 5, 2011, at 2:44 AM, Lali wrote:
(7319): p. 1061-1073).
Some of the steps you can perform through Galaxy, yet some are in development.
Thanks!
anton
galaxy team
On Apr 5, 2011, at 5:19 AM, Laura Iacolina wrote:
> Dear all,
> I’m analysing SNPs data for the first time. I tried with the few software I
> found in l
Lali:
Please, always CC mailing list when you reply.
> 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?
Which browser/OS are your using?
Thanks,
anton
galaxy
Mike:
Which parameters did you use at step 13 (if you used main site to perform these
analyses you can share your history with me).
Thanks,
anton
On Apr 5, 2011, at 2:22 PM, Mike Dufault wrote:
> Hi all,
>
> Like many people on this e-mail chain, I have been looking for advi
enerated (Operate on Genomic Intervals
-> Join).
To add to the excellent comments by Sean -> realignment and recalibration tools
are coming by this Summer together with more sophisticated genotypers.
Tx,
anton
galaxy team
On Apr 5, 2011, at 3:11 PM, Mike Dufault wrote:
> Hi Anton,
>
cloud instances (http://usegalaxy.org/cloud; although
cloud does not solve the transmission issue).
We anticipate having a Galaxy workshop in the greater LA area in the coming
months and will be glad to discuss these issues.
Thanks for using Galaxy.
anton
galaxy team
On Apr 6, 2011, at 7:13 PM
very useful)
and is based on processing on CIGAR strings in aligned SAM files. You can
simply run datasets generated by BWA through our indels tools.
Thanks and let us know if you have more questions.
anton
galaxy team
On Apr 8, 2011, at 7:42 AM, Mike Dufault wrote:
> Sean, Anton and
mapping to a set of genes?
Thanks,
anton
On Apr 11, 2011, at 11:17 AM, Daniel Elleder wrote:
> Hi,
>
> I have reads from Illumina paired-end run mapped against reference genome
> using Bowtie. Is there a Galaxy tool which would allow me to extract gene
> names from the map
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
Joanne:
1. There is no mechanism for downloading reference sequences from Galaxy at
this time.
2. I am not sure what you mean by 'Tablet'.
3. Megablast tool ('NGS: Mapping -> Megablast') will allow you to perform
comparisons against nt, wgs, and htgs databases.
Thanks f
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 hav
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&
s an issue although I
> can not recall what exactly.
Yes, if the strand is explicitly specified. If it is not specified it is
assumed to be +.
Thanks for using Galaxy.
anton
>
> Thank you in advance,
>
> David
>
>
> ___
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
somehow? Do I have to set the
type of MAF file, and to what?
Would be great if someone could give a short overview how to stitch MAF
files command-line based.
Thank you!
Anton
References
[1] Blankenberg, D., Taylor, J., Nekrutenko, A. & Galaxy Team. Making whole
ge
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 u
switching
underlying infrastructure brining much needed relief to all Galaxy users at
once.
The best venue for posting such questions is out galaxy-user mailing list
(I CC'ed it here).
Thank you and sorry for the main site troubles.
anton
On Tue, Sep 24, 2013 at 11:29 AM, Elwood Linney
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