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'm trying to use the output files from barcode splitter. I know that the command line as some wrappers made that take the output files and puts them in the history. Is there anything similar for output files but for us biologists who don't do command line? J
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I have installed an galaxy instance for purpose testing on a 8 CPU
server without problem all run perfectly.
I have made some galaxy xml wrapper to understant how galaxy calls
program and other little things.
Now I want to install a Galaxy server with a cluster configuration.
Before I have tested HTCondor but I have no Idea how I can mix Galaxy
The perfect thing was somebody have already tested this type of condor.
But I can satisfy myself with any other cluster type.
What I don't understant in fact ( maybe my worst problem ) where lie
all parts of this puzzle.
I know that I need Galaxy. I know too I need a cluster ( in my case
I understand I need something between these 2 parts ... I think
something like PBS or SGE but it's not totaly clear for me
I'm search on galaxy mailling list archive ... but I just found 2 mails
in 2008 :(
has anybody made this conf or have a configuration ?
PS : sorry for my poor english :)
When I tried to download the filtered datasets from my History at Galaxy to
my computer, I always got this error information:
"Internal Server Error
Galaxy was unable to sucessfully complete your request
An error occurred.
This may be an intermittent problem due to load or other unpredictable
factors, reloading the page may address the problem.
The error has been logged to our team. If you want to contact us about this
error, please reference the following
GURU MEDITATION: #8aa15caba14d4a3e85ce7ab069"
What is the cause for this problem? In addition, It takes about 3 to 5
minutes to refresh my Histories or to view different Histories. However, it
is very quick to refresh "Saved Histories". Is it normal?
My question is about "operating on genomic intervals, Coverage" tool. I wanted a csv list of identifiers (c4) in the second dataset that cover each interval in the first dataset.
How would I go about getting such a list?
Thank you so much in advance.
Charu Gupta Kumar, Ph.D.
I have been trying to find a solution to identify overlapping peaks between
two ChIP-Seq datasets. I have used the "Intersect the intervals of two
datasets" function, under the *Operate on Genomic Intervals* toolset -
however, I would like to be able to specify a given distance between the
peaks to still be counted as "overlapping", and this tool requires at least
1bp overlap between peaks to be counted. For example, even if two peaks
are within 500bp of each other (but don't overlap) I would like to score
this as overlapping and get the resulting genomic coordinates for
Thanks in advance for your help!
Eric Van Otterloo
I am having a problem with FastQC. When I view per base quality, it gives me a strange looking graph:
I am wondering it this is because of a problem with my data? None of my colleagues have seen this before.
Dear Galaxy Users,
I had a quick question as a new Galaxy user. I just received WGS data from Illumina where I'm given .bam files. I am not given .fastq files. Most of the Galaxy tutorials I've seen online have started with raw data in .fastq format. Can Galaxy handle if I were to upload a .bam file using the "Get Data" tool?
Furthermore are there any examples/workflows available that others have created when using Illumina data