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:
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
User name: dac330
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
University of Florida
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?
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)...
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,
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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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
Thank you very much for your help.
*Bernardo Bello Ortí*
Campus de Bellaterra-Universitat Autònoma de Barcelona
08193 Bellaterra (Barcelona, Spain)
Tel.: 647 42 52 63 *www.cresa.es *
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 ...
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.
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?