Galaxy Main public instance: data and job quotas
October 25, 2011
Dear Galaxy User,
Thank you very much for using our free and open public resource. Galaxy
has become extremely popular and as a result many people rely on it
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restric
hics, etc.) is planned for in the near-term to clarify the
functions further.
Best,
Jen
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memory I'm sucking?
Thanks!
Bryn
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a
spretus' is not, even though the SNPs
table for spretus is available. How do I use Galaxy to identify
species-specific transcripts?
Please accept my utmost appreciation,
Di
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"NR_024540"; tss_id "TSS6960";
Thanks for using Galaxy!
Jen
On 10/25/11 5:21 PM, Jennifer Jackson wrote:
Hello Carl,
Your question is similar to Olivier's, even though the problem is
presenting in a different way. There is most likely a data mismatch
problem as explaine
October 25, 2011 Galaxy Development News Brief
This release:
http://galaxyproject.org/wiki/News%20Briefs/2011_10_25
Release history:
http://galaxyproject.org/wiki/News%20Briefs
Source: http://getgalaxy.org
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; Hi Jennifer,
>
> I have sequenced one sample on 2 lanes of GAII, and now I am trying to
> merge the 2 fastq files. How should I do it on Galaxy? Thank you very
much!
>
> Best,
>
> Tracy
>
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; Hi Jennifer,
>
> I have sequenced one sample on 2 lanes of GAII, and now I am trying to
> merge the 2 fastq files. How should I do it on Galaxy? Thank you very
much!
>
> Best,
>
> Tracy
>
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; Hi Jennifer,
>
> I have sequenced one sample on 2 lanes of GAII, and now I am trying to
> merge the 2 fastq files. How should I do it on Galaxy? Thank you very
much!
>
> Best,
>
> Tracy
>
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ice provider actually just split my PE files by lines
(not no. of reads ) in fastq
assuming that I can't merge them in galaxy, I am merging them properly
then splitting them again (anyway i can map using concurrent processes
and merged the bam later on
Cheers
Kevin
On Fri, Oct 28, 2011 at 10:30
analysis, on paired-end data ?
Yes, this options is included on the CuffDiff tool form as an option.
Paired vs mate paired data questions would be best directed to the tool
authors at tophat.cuffli...@gmail.com.
Best,
Jen
Galaxy team
Thanks
Danny
On 10/27/11 4:56 PM, "Jennifer Ja
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Galaxy team
On 10/25/11 11:24 PM, GANDRILLON OLIVIER wrote:
Hello Jennifer
Le 26/10/11 02:15, « Jennifer Jackson » a écrit :
Hello Olivier,
Are you using a reference gene annotation GTF file?
Well if I do , I do not know :-)
What I used is first TopHat and then Cufflink. At what stage shall
Hello,
I have removed you from galaxy-user. Instructions to manage list
membership is at the bottom of this and all mailing list messages.
In short, through this link:
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Is best not to post to the mai
NR_* into protein id, like NP_? I do not know. Could you please tell me?
Thank you very much!
Victor
From: Jennifer Jackson [j...@bx.psu.edu]
Sent: Thursday, October 27, 2011 11:23 PM
To: Li, Jilong (MU-Student)
Cc: galaxy-u...@bx.psu.edu
Subject
does one need any additional information?
Best regards
Kaisa
From: galaxy-user-boun...@lists.bx.psu.edu
[galaxy-user-boun...@lists.bx.psu.edu] on behalf of Jennifer Jackson
[j...@bx.psu.edu]
Sent: 28 October 2011 19:42
To: Benoit HENNUY
Cc: gal
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De: galaxy-user-boun...@lists.bx.psu.edu [galaxy-user-boun...@lists.bx.psu.edu]
Em Nome De Jennifer Jackson [j...@bx.psu.edu]
Enviado: quinta-feira, 27 de Outubro de 2011 21:23
Para: Benoit HENNUY
Cc: galaxy-u...@bx.psu.edu
Assunto: Re: [galaxy-user] get data
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xception reports here)
I somehow don't think the user's supposed to see the "error logs" or exception
reports, so what next?
Clare
- Original Message -
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Cc: galaxy-u...@bx.psu.edu
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ay to go.
Thank you and hope to hear from you soon,
Klaudyna
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each
output file (i.e. the multiple ones output from cuffdiff) within galaxy
is very inefficient and time consuming.
Thanks.
Rich
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ht
extension. or i
should try other compressed file extension.
xaingmimg
Quoting Jennifer Jackson :
Hello Xiangmimg,
Data files can be loaded using a URL on the "Get Data => Upload" form.
FTP and HTTP connections are supported. This is briefly described on
that form.
If you are still
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ith my log in info
Thanks
Shamsher
On Tue, Nov 8, 2011 at 5:36 AM, Jennifer Jackson mailto:j...@bx.psu.edu>> wrote:
Hi Shamsher,
Are you by chance working with more than one open Galaxy browser
window at a time? Doing this is not recommended as it can cause
confusing
y
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ht)
orientations. I've pasted the beginnings of the two files below my
signature in case this is useful for diagnosing the problem.
Can anyone tell me what I'm doing wrong? Thanks,
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11/9/11 4:25 AM, Ian Donaldson wrote:
Cistrome (instance of GALAXY) has CEAS included.
Ian
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[j...@bx.psu.edu]
Sent: 08 November 2011 22:43
To
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anks,
Oren
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option will work for your
project,
Best,
Jen
Galaxy team
On 11/11/11 4:06 PM, Jennifer Jackson wrote:
Hi Aurelie,
Would you have time to share a history link containing the two types of
datasets for me? Use "Options -> Share or Publish", generate the link,
then email it back t
my files.
thaks
Diana Trejo, PhD
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November 18, 2011 Galaxy Development News Brief
This release
http://galaxyproject.org/wiki/News%20Briefs/2011_11_18
Release history
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Source http://getgalaxy.org
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using "delete permanently". But my usage did not go down at
all. Is there a delay in this happening, or is there some way to purge
the files?
richard
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*From:* Jennifer Jackson
*To:* Richard Mark White ; "galaxy-u...@bx.psu.edu"
*Cc:* closetic...@galaxyproject.org
*Sent:* Wednesday, November 30, 2011 1:09 PM
*Subject:* disk quota not updating
Hi Richard,
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one other question about using a
custom reference genome. Is it possible to use an annotated genome as
the reference for a Bowtie alignment? Using a genome in fasta format is
only so helpful.
Thanks,
Matt Biggs
On Mon, Dec 5, 2011 at 8:24 AM, Jennifer Jackson mailto:j...@bx.psu.edu>>
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http:
rry. I just want to
check I haven't missed anything, since sibling tools from e.g. the
samtools and picard suites are wrapped.
Thanks,
Clare
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Galaxy, but I'm not
sure how to combine all the fa files into one file. The Zebrafish genome from
Ensembl comes in 27 separate .fa files. How do I combine these so that when I
upload them to Galaxy, I can use the whole genome as my reference genome?
Thanks,
Sheena
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find information on how many total reads went into TopHat? How many
reads were removed? How many unique hits to reference genome?
I was trying to prepare a table for presentation and realize that I
could NOT find the information in my GALAXY account?
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Jennifer Jackson
er.
>
> What I would like to do is to be able to edit the bed file to change
the text MACS_peak_ to, say, treatment1_peak_ so that
peak 20 would now still be numbered 20 in both files, but would have a
different label. This would be pretty easy to do using regular
expressions and
se
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Jennifer Jackson
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of
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Jennifer Jackson
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Jennifer Jackson
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Jennifer Jackson
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