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
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)...
Is there a currently a known problem with the "export to file" function?
I'm trying to migrate some data from the public galaxy to a private one;
the export function worked well with a small (~100mb) dataset, but it has
not been working with larger datasets (>2GB) and I get the error: Server
Error. An error occurred. See the error logs for more information. (Turn
debug on to display exception reports here). Is there a limit on the file
size of the export? If so, what is it?
Thanks in advance,
I am interested in using Cufflinks 2.0 on our local instance of Galaxy but I am not sure if it is supported yet. We did Galaxy update in early October and we tried to install cufflinks V2.0 and it seems to run. I get the output files and they have the genes listed but 0.000 for all results (using files that worked on previous version).
The output file summaries contain the following:
Info: ERROR: Unable to read builds file: [Errno 2] No such file or directory: '/opt/galaxy/galaxy-dist/lib/galaxy/util/../../../tool-data/shared/ucsc/publicbuilds.txt'
ERROR: Unable to read builds file: [Errno 2] No such file or directory: '/opt/galaxy/galaxy-d
Is there a fix for this error or do we need to go back to the latest supported version of Cufflinks and if so which version?
I am about to write a syncing tool for Galaxy like Dropbox using Python
with the progress bar. How do I integrate it with galaxy? It would be easy
for client to upload files using the syncing tool. Are there any syncing
tools available for Galaxy?
I would like to know if it is possible to manage libraries permissions
with the API galaxy, and how to do that.
Thank you for your answer,
Fabien Mareuil | Centre d'Informatique pour la Biologie
fabien.mareuil(a)pasteur.fr | Institut Pasteur
25,28 rue du Docteur Roux 75015 Paris, France
This may be a little different question from usual Galaxy use, I have
alist of Transfec binding matrix ids -v$1234.... and want to extract
bidning sequences corresponding to these ids. Is it possible to extract
such sequences with in Galaxy or anyone aware of an alternative approach
please. I understand that with genomic coordinates I can extract the
sequences in galaxy but I dont see the genomic coordinates.