Using full path in the ini file fix the problem!
Thanks,
Yupu
On Jan 30, 2014, at 10:21, Jennifer Jackson wrote:
> Hi Yupu,
>
> I'm sorry, I mixed up the processing for custom builds with the processing
> for installed builds in my initial reply. A .2bit & .len file are appropriate
> for what
Yupu,
Very glad! The thanks goes to Jeremy who sorted out the issue.
We had some big changes the last few release cycles, and unexpected
issues popped out. It was very nice of you to not only take the time to
report the problem, but to also follow up with sending feedback until
resolved.
If
Hi Yupu,
I'm sorry, I mixed up the processing for custom builds with the
processing for installed builds in my initial reply. A .2bit & .len file
are appropriate for what you are doing - and the wiki instructions are
accurate.
Still, I double checked with Jeremy, the scientist that developed
Hello Yupu,
Using a .len file is problematic at this time. In the upcoming release
this will be corrected. Using a .fasta file is the solution. In many
cases, using a .fasta file can be preferred as it will include the
reference genome sequence in the visualization, but the choice is yours,
o
Yes I have restarted my Galaxy many times and I have also tried different
genome build such as hg18 and experience the same problem.
Yupu
On Jan 29, 2014, at 3:32, Hans-Rudolf Hotz wrote:
> Hi Yupu
>
>
> Just double checking: Have you restarted your Galaxy server after adding the
> len files
Hi Yupu
Just double checking: Have you restarted your Galaxy server after adding
the len files?
Regards, Hans-Rudolf
On 01/28/2014 08:12 PM, Yupu Liang wrote:
Hi,
I am trying to set up the visualization functionality on our local Galaxy
installation. I followed the instructions on
htt
Hi,
I am trying to set up the visualization functionality on our local Galaxy
installation. I followed the instructions on
https://wiki.galaxyproject.org/Visualization%20Setup
And here is the list of len files:
ls -l tool-data/shared/ucsc/chrom/
total 200
-rw-rw-r-- 1 galaxy galaxy10 Jan 2
Hi Jen,
I just tried it again. Just in case I cleared my browser, Firefox, cache,
history and cookies, although not memorized passwords. The saved
visualization gave me the Guru mediation error ,
GURU MEDITATION: #202b9e1bd2a8460a8089153f0853e7f4,
and when trying to visualize a bam file I g
Hi Ann,
I was not able to duplicate the behavior, but the way visualizations are
launched and the time frame in our logs are both a fit with an earlier
known job scheduling delay on the public Main instance. Please try the
visualization again, if you haven't already, and let us know if it is
Hi,
Earlier today I couldn't add a new visualization. I just was working again
and now I cannot load the viualizations that I'd previously set to load (BAM
from SAV). I get the message
Internal Server Error
Galaxy was unable to sucessfully complete your request
GURU MEDITATION: #ff39a25
Hello Peggy,
The reference genome named simply "arabidopsis" in Galaxy is a legacy
genome name and may not work with all tools. Assigning the reference
genome name "Arabidopsis_thaliana_TAIR9" instead is the recommended
choice (both are TAIR9).
The next item to change is the format of the ch
Hi All,
I am new of Galaxy. I want to visualize my short mapping results in the browser.
I uploaded my .wig file which has format as this, (first column is position,
second is the read soverage of that position)
variableStepchrom=Chr1
4 1
5 1
6 1
7 1
8 2
9
You can just type the first few letters of your organism to go through the
list quickly.
-Farhat
--
Farhat Habib, PhD
Scientist-C, Center of Excellence in Epigenetics
Indian Institute of Science Education & Research, Pune
http://www.iiserpune.ac.in/~farhat
Twitter: @far_hat
Office: +91 20 2590 80
Oh btw I just looked at the list of loaded system-installed builds. there
are 934 genomes if I am not wrong.
browsing 5 by 5 is quite excruciating!
On 6 September 2011 21:00, Kevin Lam wrote:
> I found the dropdown menu list to be too long to be effectively used
> especially when viewed i chrome
I found the dropdown menu list to be too long to be effectively used
especially when viewed i chrome (browser) I can only see 5 genomes at a time
and the ordering of the genomes isn't intuitive.
Can I suggest that a frequently used genomes list be in the rest of the page
so that it is easier to use
===> Please use "Reply All" when responding to this email! <===
Hi Jen, I have been using the following link for learning to visualize TOPHAT
results:
http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise
How can get the RefGENE for the whole human genome instead of Ch19 listed
Hi jen, I have used BOWTIE to align my RNA-seq reads to HSV2 genome; out
of 35,000,000 lines, only 621 lines left when I chose to have mapped
reads only. How can visualize these aligned reads to HSV-2 genome?
In the panel of converted SAM to BAM, I tried to use the data in
trickster, but I am not
Hello Tao,
For the Bowtie results, the aligned results may be low because the data
is RNA and not DNA. TopHat is generally considered a better choice for
RNA since it allows for bridges over splice sites (introns). The full
documentation for each program is on each tool's form and/or you can
ck on: 'Visualization -> 'New Track Browser' -> 'Add a Custom Build'
>
>
> Hope this helps.
>
> Regards, Hans
>
>
> On 08/04/2011 01:51 AM, vasu punj wrote:
>> IGV should allow you to do this but not sure about trackbrows
allow you to do this but not sure about trackbrowser in Galaxy.
Vasu
--- On Wed, 8/3/11, Jiannong Xu wrote:
From: Jiannong Xu
Subject: [galaxy-user] visualization
To: "galaxy-user@lists.bx.psu.edu"
Date: Wednesday, August 3, 2011, 6:03 PM
Hi Jen,
I mapped illumine reads to draft gen
I use IGV outside of Galaxy. If you download your bam and bam index
files you can load those and your reference into IGV to visualise them.
On 04/08/2011 00:03, Jiannong Xu wrote:
Hi Jen,
I mapped illumine reads to draft genomic contigs, and try to visualize the
mapping. Is there any way I ca
IGV should allow you to do this but not sure about trackbrowser in Galaxy.
Vasu
--- On Wed, 8/3/11, Jiannong Xu wrote:
From: Jiannong Xu
Subject: [galaxy-user] visualization
To: "galaxy-user@lists.bx.psu.edu"
Date: Wednesday, August 3, 2011, 6:03 PM
Hi Jen,
I mapped illumin
Hi Jen,
I mapped illumine reads to draft genomic contigs, and try to visualize the
mapping. Is there any way I can use my own reference contigs for visualization?
Thanks
John Xu
NMSU
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