Help with Summary Statistics
by D. A. Cowart
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:
>HD4AU5D01BHBCQCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC
>HD4AU5D01A093MCTCTGTCGCTCTGTCTCTCTTCTCTCTCTCTCTCTCT
etc...for each species
I have attempted to use the "Summary Statistics" button, however it
appears to only be for numerical data and not sequence data. Is this
tool/task available
via Galaxy?
Thank you,
Dominique Cowart
User name: dac330
6 years, 4 months
SNP finding
by Xiefan Fang
Dear galaxy users,
We have done deep sequencing on some known genomic loci using
Hiseq2000. I have already mapped the reads to the reference sequences by
using Galaxy. In the next step, I want to find SNPs and calculate the SNP
percentage within the reads. There are 500,000 to 1,000,000 reads per
biological sample. Can I do it with galaxy? If not, is there other programs
available in windows? Considering that I am not very familiar with
programming.
Thanks,
Xiefan
University of Florida
6 years, 10 months
extracting a subset of sequences from a very large fasta file(1.5 million)
by Perumal Vijayan
I have successfully uploaded a large fasta file (2.5 million genomic
sequence contigs) onto Galaxy server. I wish to extract a subset of
sequences from this file. I have a list of the fasta headers. Is there a
way I can accomplish this on Galaxy?
--
Perumal Vijayan
Saskatoon
Canada
7 years, 7 months
Nominate topics for the 2013 Galaxy Community Conference (GCC2013) Training Day
by Dave Clements
Hello all,
Nominations are now open <http://bit.ly/gcc2013nom> for Training Day
topics<http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay>at the
2013
Galaxy Community Conference
(GCC2013)<http://wiki.galaxyproject.org/Events/GCC2013>.
GCC2013 <http://wiki.galaxyproject.org/Events/GCC2013> will start on 30
June with a Training Day featuring 4 parallel tracks, each with three, two
hour workshops, for a total of twelve sessions.
Any topic of interest to the Galaxy Community can be
nominated<http://bit.ly/gcc2013nom>(see what
was offered at GCC2012<http://wiki.galaxyproject.org/Events/GCC2012/TrainingDay>).
Topics can be repeats from last year or brand new, and you are encouraged
to nominate as many topics as you like. The 2013 Galaxy Community
Conference (GCC2013) <http://wiki.galaxyproject.org/Events/GCC2013> will
start on 30 June with a Training Day featuring 4 parallel tracks, each with
three, two hour workshops, for a total of twelve sessions. Nominations will
be compiled into a uniform list, and then topics will be voted on by the
Galaxy Community starting in late January.
Topic nomination closes 11 January.
Thanks,
Dave Clements, on behalf of the GCC2013 Organizing
Committee<http://wiki.galaxyproject.org/Events/GCC2013/Organizers#Organizing_Committee>
Links:
http://bit.ly/gcc2013nom - nominate a topic
http://bit.ly/gcc2013td - Training Day page
http://galaxyproject.org/GCC2013 - Conference home page
http://bit.ly/gcc2013prom - help get the word out
--
<http://galaxyproject.org/wiki/GCC2012>http://galaxyproject.org/
http://getgalaxy.org/
http://usegalaxy.org/
http://wiki.galaxyproject.org/
7 years, 8 months
Re: [galaxy-user] Batch jobs...
by Neil.Burdett＠csiro.au
Do i need to modify a setting in universe_wsgi.ini or somewhere then ? As I attach screenshots of what I've got (I have a recent subversion checkout)...
Thanks
Neil
[cid:image001.jpg@01CDB754.FC6C6330]
[cid:image002.jpg@01CDB754.FC6C6330]
7 years, 8 months
galaxy cloudman login
by Sun, Wenping [USA]
Hello,
I have galaxy cloudman running and had tried one time success to log in to retain the previous data and history after re-launching followed by 1st time restart. Today I am re-launching again along with the correct size of ebs volumes that I adjusted earlier. However, my login is not recognized at all ("error:no such user...."). I tried several time of terminating and restarting and it is still the same. My admin which is same as the login was able to retained every time. What's the issue with the log in??
It is taking time to repeat previous data/history. I need your help to retrieve my login.
Thank you in advance,
Kathryn
7 years, 9 months
incompatible frame
by Barbara Bryant
I'm having trouble viewing SeqPos output; I get "Please use a frames compatible browser when viewing this output" - yet I can see other frames in the browsers. Tried IE, Chrome, Firefox. Any suggestions? Thanks!
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For more information about Constellation, please visit us at http://www.constellationpharma.com.
7 years, 9 months
Pipeline design for bacterial RNA-Seq
by Bernardo Bello
Hi community,
I have just discovered a wonderful Galaxy server for RNA-Seq analysis:
Oqtans http://galaxy.raetschlab.org/. I am impressed by the huge quantity
of useful tools that they have integrated there.
I'm dealing with bacterial transcriptome analysis. We have the genome
sequence of this bacteria.
RNA samples are now been sequenced and I am designing a pipeline for data
analysis. I would like you to suggest me the tools that I can/should use in
order to analyse my data. My sequences come from Ion Torrent platform. For
each sample I have a fastQ file of about 3 million sequences. They are less
than 200 bp and have a mean of 150 bp. I you need more information please
ask me.
Thank you very much for your help.
Regards, Bernardo
--
*Bernardo Bello Ortí*
PhD student
CReSA-IRTA
Campus de Bellaterra-Universitat Autònoma de Barcelona
Edifici CReSA
08193 Bellaterra (Barcelona, Spain)
Tel.: 647 42 52 63 *www.cresa.es *
*
*
7 years, 9 months
running out of disk space in cloudman instance
by Siddhartha Basu
Hi,
The instance ran out of space very quickly as soon as i import ~4 3GB fastq
file. The problem turns out to be identical as described here ...
http://gmod.827538.n3.nabble.com/Re-galaxy-user-Problem-using-Galaxy-on-t...
Is there any permanent fix available that is already baked into the
entire cloud setup and workflow.
For the time being, i circumvent the issue by mounting the /tmp in a
separate ebs volume partition(~50GB), adding it in /etc/fstab and then
reboot the machine. However, the /tmp has to be mounted without *noexec*
option since the upstart python script executes another python script(cm_boot.py possibly)
from /tmp to start the cloudman webapp.
thanks,
-siddhartha
7 years, 9 months
galaxy cluster nodes from the cloudlaunch site
by Sun, Wenping [USA]
Dear Galaxy users,
I created galaxy instance using galaxy ami the first time. When I re-launch via cloudlaunch site the 2nd time, I have question on adding cluster nodes. There are several pull-down options for the nodes type, no matter which type I choose, they always generate nodes with only 15gb. Is there other option I can have option to define the root space for the nodes?
Thank you,
Kathryn
7 years, 9 months
