Fastq groomer has Solexa or Illumina 1.3+ as an input quality format. I
asked at the sequencing facility about their machine and output and they
said their format was Illumina 1.8+ (the newest). I tried to convert my
fastq file into Sanger by fastq groomer, using Illumina 1.3+ as an input
option and got all reads with quality of around 10... Does it mean that
Galaxy cannot be used on a dataset with 1.8+ encoding or something else was
I uploaded (on Oct, 25) data through FTP site and I was not able to
retreiven them to include them in a history. I suppose that the files
should appeared in the FTP list under the Get data page.
THese data are named "P2 fastq .gz" files that I wold like to use in RNA
Thank you to help me to be able to use these data.
University of Liege
Regarding the GTF files for cuffllinks, how do I obtain one for all
human mRNA that actualy contains gene names rather than accession
numbers. I went to the UCSC table browser but their files contain
accession numbers that I dont know how to decode en-masse.
I've been using galaxy to analyze maf files and today the drop down list for database/builds for genomes has lost most of the genomes once listed.
I no longer see any bacteria or plants on the list, specifically TAIR9 arabidopsis is no longer on the drop down list when it was just yesterday. Did something change?
Hi, I'm trying to use the SAM/Filter pileup analysis on some pileup output files I've uploaded. But when I click the analysis link, these output files don't appear in the Select dataset dropdown menu; instead only one file, the output from FASTQ Summary Statistics which is obviously not pileup output, is shown.
Would you please add Staphylococcus aureus strain Newman to your database? Workflows to analyze data for genomes available through your database are really simple - but I must admit that I've been struggling with trying to get this to work for a genome (and in particular with the annotation) that I've uploaded myself.
Thanks for the help and the continued support!
Joe J. Harrison
Department of Microbiology
University of Washington
I installed the Amazon Galaxy CloudMan today but am not able to load any of
the Galaxy AMIs. The AMI on the user galaxy webpage does not exist, but 3
AMIs do. I tried the 2 most current ones and they don't load:
It looks like everything is fine on the Amazon side:
Thanks for your help,
We encountered queuepool limit problem after running the workflows for a few times.
We have tried to increase these 2 parameters: database_engine_option_pool_size and database_engine_option_max_overflow to 20 and 40 respectively.
Are there other parameters that we can change?
I wasn't sure whether to send this to galaxy-dev or galaxy-user. I'm
having a problem launching a Galaxy instance on Amazon. I have done
this in the past with no problems. I suspect I'm doing something
trivial wrong but can't work out what!
The problem is that after starting the instance, when I go to
http://public-dns-url/cloud and the "Initial Cluster Configuration"
window pops up, the initial storage size text box is disabled. That
is, the text box after the first radio box ("Galaxy Cluster") is
greyed out. So, I can't enter a size for the storage and if I just
proceed without doing so, it (I think) causes CloudMan to fail.
I thought I was probably just having browser issues but I get the same
problem repeatedly in Chrome and Firefox. When I inspect the element,
I see <input disabled="true" ... name="g_pss"...> so I think it really
is disabled. This seems like a weird problem so I suspect it's me, but
I can't work it out. Any help would be appreciated!
P: 03 903 53357
M: 0414 854 759