Hello Meike,
We had a known period of delay last week - hopefully your job was able
to processes in the time since then. This is how you can determine a
job's status:
https://wiki.galaxyproject.org/Support#Dataset_status_and_how_jobs_execute
The Main site is down right now, but watch our @gal
Hi Maria,
I didn't notice any obvious problematic usage, format, or content issues
with the Tuxedo pipeline execution in your history. Your protocol is
right on track. This leaves data and parameter inputs to consider.
I did notice that you are mainly using defaults and omitting the use of
r
Hi Maria,
More details are needed to help. Would you like to share a history with me?
You might also find the tutorials and other resources for RNA-seq
analysis we have helpful. Many are linked from here:
https://wiki.galaxyproject.org/Support#Tools_on_the_Main_server:_RNA-seq
I've also added
Hi Pasquale,
From a quick look (and I am not the tool-building expert of our team!),
I suspect that the problem is with the "format" assigned to the output
of the first tool, and input of the second tool. Specifically,
"format=string" is problematic, unless you have also defined this in
your
Hi Seung Hee,
You can request that this tool be added to the public Main server at
usegalaxy.org through Trello and the team will consider it. For right
now, the options are local or cloud. (as in my other reply)
Or, you can look around the the other public servers hosted by our
community -
Thanks Peter for another option!
Jen
Galaxy team
On 11/23/13 6:19 AM, Peter Cock wrote:
On Fri, Nov 22, 2013 at 8:48 PM, Jennifer Jackson wrote:
Hi Seung Hee,
I know we discussed this on the other list, but I didn't point you to the
open development ticket to (potentially) extend the functio
Thanks Geert,
This tool was in the back on my mind, but I couldn't find it last
week for some reason!
Seung Hee - this is a very good choice, for use in a local or or cloud
Galaxy.
http://getgalaxy.org
http://usegalaxy.org/cloud
I think I will close out the ticket below and point it to Cu
You might also use ( / add to main) the CutAdapt tool, which is
available in the main toolshed. It takes multiple adapters, allows
3/5/both side adapters, and is fast.
http://toolshed.g2.bx.psu.edu/repository/view_repository?sort=User.username&operation=view_or_manage_repository&id=f19bc86bac94
On Fri, Nov 22, 2013 at 8:48 PM, Jennifer Jackson wrote:
> Hi Seung Hee,
>
> I know we discussed this on the other list, but I didn't point you to the
> open development ticket to (potentially) extend the functions of the "Cut"
> tool. This is not being actively worked on right now, but you can fo
Hi Seung Hee,
I know we discussed this on the other list, but I didn't point you to
the open development ticket to (potentially) extend the functions of the
"Cut" tool. This is not being actively worked on right now, but you can
follow it for updates if you want.
https://trello.com/c/CbFSHrU5
Hi Luis,
There are a few options:
The tool " Phenotype Association -> SIFT" will accept an input file of
variant locations/alleles and retrieve annotations, including OMIM
Disease associations.
Alternatively, you could label your variants by rs identifiers (or
perhaps you already have these
Hello Jianguang,
The RNA-seq tutorial was just updated:
http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise
Hopefully this helps,
Jen
Galaxy team
On 8/9/12 10:41 AM, Du, Jianguang wrote:
I have RNA-seq datasets of several cell types. I want to compare
alternative splicing e
On Thu, Aug 2, 2012 at 7:50 PM, D. A. Cowart wrote:
> Hello,
>
>
> I am attempting to use Galaxy to calculate the mean sequence read length and
> identify the range of read lengths for my 454 data. The data has already
> been organized and sorted by species. The format of the data is as follows:
>
Hi Noa,
This is it exactly - thanks for adding in the interpretation!
Jen
On 5/10/12 11:54 AM, Noa Sher wrote:
I think the sign is to show if it is x-fold more than the first
condition (+) or x-fold less than the first condition (-). A regular
fold would give you values from 1-whatever if samp
I think the sign is to show if it is x-fold more than the first
condition (+) or x-fold less than the first condition (-). A
regular fold would give you values from 1-whatever if sample 2 is
more than sample 1, and a fraction (0-1) if sample 1 is expressed
more t
Hi Jiwen,
As far as I know, this is possible. The CuffDiff log2 value is defined
here: http://cufflinks.cbcb.umd.edu/manual.html#gene_exp_diff
7 FPKMx 8.01089 FPKM of the gene in sample x
8 FPKMy 8.551545 FPKM of the gene in sample y
9 log2(FPKMy/FPKMx) 0.06
Hello Tilahun,
Are you logged into your Galaxy instance UI using your admin account?
This will display the Admin menu.
Admin permissions are set up in the universe_wsgi.ini file:
# -- Users and Security
< other items >
# Administrative users - set this to a comma-separated list of valid Gal
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 o
Hi Jiwen,
The bioinformatics part of your analysis sounds as if it went fine, so
that is good news. This list may not be the best place to get feedback
about library construction methods, but we can see who has help to offer.
I did a quick search myself and found this recent publication that
Hello Jiwen,
You would have to compare this with your regular transfer speed, but
this does seem to be on the low side. Galaxy being busy could have some
influence on transfers, but not at the level that you are reporting.
I just ran a test using FileZilla and transferred a 56M file in a litt
>
> Brand new galaxy user here.
>
> I ran an RNA-seq Illumina experiment in which I compare cells from wild
> type animals and cells from animals that have a deletion in a splicing
> factor. Now I have my data in fastq format and need to do analysis to
> figure out which transcripts are changed and
Hi Zach,
Would you have time to send this in as a bug report so that we can take
a closer look? Format problems are likely the issue, but this can be
double checked. To report as a bug, click on the green bug icon in the
error dataset's box in your history. If your Galaxy account uses a
diffe
You could try "fasta width formatter" on your reference fasta. This has
helped me in the past when I received a similar error.
On Tue, Sep 13, 2011 at 11:32 AM, Zachary A Lewis wrote:
> Hi,
> I was wondering if someone could help me with an error message I'm getting
> after performing a sam to
Hi Mike,
I just started a brand new instance with an account that is different from
the one used to create required AWS components and Cloudman came up just
fine, having started all of the required services.
Not that it should matter much, but are you instantiating a brand new
instance or recoverin
the) BAM file once I get it
> to my local machine. Each step is one step closer.
>
> Thanks again,
> Mike
>
>
> --- On *Fri, 4/15/11, Enis Afgan * wrote:
>
>
> From: Enis Afgan
> Subject: Re: [galaxy-user] Help!! with Galaxy Cloud!
> To: "Mike Dufa
.dat file?
Thanks again,
Mike
--- On Wed, 4/13/11, Enis Afgan wrote:
From: Enis Afgan
Subject: Re: [galaxy-user] Help!! with Galaxy Cloud!
To: "Mike Dufault"
Cc: galaxy-u...@bx.psu.edu
Date: Wednesday, April 13, 2011, 11:15 PM
Hi Mike, Once the given EBS volume is at
able to see all of the .dat files in /mnt/galaxyData. What
> commands can I use to download a file to my HD? Also, what program should I
> use to open the .dat file?
>
> Thanks again,
>
> Mike
>
> --- On *Wed, 4/13/11, Enis Afgan * wrote:
>
>
> From: Enis Afgan
Hello again,
So I am able to see all of the .dat files in /mnt/galaxyData. What commands can
I use to download a file to my HD? Also, what program should I use to open the
.dat file?
Thanks again,
Mike
--- On Wed, 4/13/11, Enis Afgan wrote:
From: Enis Afgan
Subject: Re: [galaxy-user] Help
; HD?
>
> Thanks,
> Mike
>
> --- On *Wed, 4/13/11, Enis Afgan * wrote:
>
>
> From: Enis Afgan
> Subject: Re: [galaxy-user] Help!! with Galaxy Cloud!
> To: "vasu punj"
>
> Cc: galaxy-u...@bx.psu.edu
> Date: Wednesday, April 13, 2011, 10:01 AM
>
the EBS to that cluster. I also established an ssh
to the Unis cluster but I do not know where to find the BAM file. Do you know
how I can access the BAM file so that I can transfer it to my local HD?
Thanks,
Mike
--- On Wed, 4/13/11, Enis Afgan wrote:
From: Enis Afgan
Subject: Re: [galaxy-
gt;
>
> From: Enis Afgan
> Subject: Re: [galaxy-user] Help!! with Galaxy Cloud!
> To: "Mike Dufault"
> Cc: galaxy-u...@bx.psu.edu
> Date: Tuesday, April 12, 2011, 9:31 PM
>
>
> Galaxy has the functionality to recover any jobs that were running after
> i
ore or did it relauch when you restarted Galaxy? I
just don't know if the analysis would be compromised.
Thanks again to you and the whole Galaxy team.
Best,
Mike
--- On Tue, 4/12/11, Enis Afgan wrote:
From: Enis Afgan
Subject: Re: [galaxy-user] Help!! with Galaxy Cloud!
To: &quo
nks again to you and the whole Galaxy team.
>
> Best,
>
> Mike
>
> --- On *Tue, 4/12/11, Enis Afgan * wrote:
>
>
> From: Enis Afgan
> Subject: Re: [galaxy-user] Help!! with Galaxy Cloud!
> To: "Mike Dufault"
> Cc: "Anton Nekrutenko&q
am.
Best,
Mike
--- On Tue, 4/12/11, Enis Afgan wrote:
From: Enis Afgan
Subject: Re: [galaxy-user] Help!! with Galaxy Cloud!
To: "Mike Dufault"
Cc: "Anton Nekrutenko" , galaxy-u...@bx.psu.edu
Date: Tuesday, April 12, 2011, 9:16 PM
Ahh, for some reason cloudman is thinkin
t; know how to access the Analysis window.
>
> Is there a way back into my analysis?
>
> Thanks,
> Mike
>
>
>
> --- On *Tue, 4/12/11, Enis Afgan * wrote:
>
>
> From: Enis Afgan
> Subject: Re: [galaxy-user] Help!! with Galaxy Cloud!
> To: "M
analysis?
Thanks,
Mike
--- On Tue, 4/12/11, Enis Afgan wrote:
From: Enis Afgan
Subject: Re: [galaxy-user] Help!! with Galaxy Cloud!
To: "Mike Dufault"
Cc: "Anton Nekrutenko" , galaxy-u...@bx.psu.edu
Date: Tuesday, April 12, 2011, 8:55 PM
Hi Mike, Try accessing your Ga
Hi Mike,
Try accessing your Galaxy instance now. It should be ok.
The link in your email contained the IP for your instance so I took the
liberty of restarting Galaxy and that brought it back up. There seems to
have been an issue with Galaxy accessing its database and that resulted in
Galaxy crash
Hello Galaxy Staff,
My data has been running on the Amazon EC2 for just over 24hrs. I have not
closed any windows and my Exome analysis made it all the way through to filter
on Pile up. I have two tabs for this instance. One is the Galaxy Cloudman
Console and the other is the tab where I perfor
Hi Dan,
The problem is that your FASTA file has a blank lines in it (the first
is line 448). You can get rid of them within Galaxy with the Select
tool (under Filter and Sort). Select the NOT Matching option and enter
"^$" (without the quotes) into the pattern box. This will remove all
li
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