I'm interested in using the Genomic Diversity tools. I've used these
with success for a previous project. For this current project, I've
converted a vcf file (29 subjects) to a gd_genotype file. When I attempt
to specify individuals, the checkboxes for each subject are not present.
Without specifying individuals, I am unable to complete other analyses
(overall FST, etc.)
I cannot distinguish a difference between the vcf files that were
successful from the previous project and this current project's vcf, but
I assume there is a format difference that I cannot detect.
I'm using Galaxy at the main site. I executed the jobs on Fri Feb 21
22:09:49 2014 (UTC). I can share the histories of the projects if necessary.
Michael J. Montague, Ph.D.
Post-Doctoral Research Associate
The Genome Institute, Washington University School of Medicine
4444 Forest Park Avenue, Campus Box 8501
St. Louis, MO 63108
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I am unable to upload more than 3 GB data from local computer to local
installation of galaxy.
How can I do that ?
I saw many of the tutorials which says about online upload.
My Galaxy is running on 127.0.0.7:8080
I tried FileZilla to upload file, but its says
"Connection established, waiting for welcome message"
and after some time
I would like to perforn my SNP calling pipeline (for MySeq Illumina
reads) to previously sequenced and assembled genomes.
Is there any read simulator in the Main Galaxy?
I am looking for something like the wgsim algorithm in SAMtools...
Yes, you are correct, the count files only address a portion of the new
features. Recent updates to the underlying tools in the Tuxedo suite
have resulted in issues of this sort as well (among others). The current
plan is to continue with development to enhance the tool wrappers in
Galaxy to support as much downstream analysis as practical. I created a
new ticket as a catch-all to address this need in a global way. Details
will be added as work progresses. https://trello.com/c/ugu8dty0
This is a timely and important inquiry. Our user & development community
feedback is an important component in how work is prioritized. _/I
encourage you and others interested in this enchantment to "up-vote" the
ticket/__/in Trello./_ Comments are also welcome. Trello help:
On 2/18/14 5:45 AM, Dottorini, Tania wrote:
> Hi Jennifer,
> Thanks for your help, I did my Cuffdiff runs on 2/12/2014 but still I was not able to analyse replicates by CummerBund. The output of replicates(cuff) is empty.
> Thank you
I am attempting to megablast a FASTA file containing ~45,000 records of 100nt each against the nt database using the Galaxy web interface. I am using a Galaxy-generated FASTA file produced from a groomed FASTQ file using the 'FASTQ to tabular' and 'Tabular to FASTA' tools. When I try to use this as input for the Megablast tool, I get the "Required metadata values are missing" error. When I look at the attributes of the FASTA file, the datatype is indeed set to FASTA. I have tried downloading the FASTA file and reuploading it as a FASTA file explicitly with the same result. I also tried changing the FASTA width to 79, and trimming the records to 70nt each – not the problem. If I make a file containing only the first FASTA record, I get the same error. Any suggestions?
My name is Eva, and Im researcher in FHUC-UNL Argentina. My work is in
population genetics of freshwater fishes. I use microsatellite loci to test
genpop data. I was wondering if Galaxy contains STRUCTURE software
(Bayesian method to define number of clusters in a sample). If the answer is
yes, ¿How should I use it?
Thank you so much for your help,
Dra. Eva Rueda
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I would like to disable seeding when doing a sequence mapping using bwa.
Apparently, this is commonly performed using the aln -l option set at a
value higher than the read length, and is often set at values above 1000. In
Galaxy, the default option is -1 for this parameter, and it is indicated
that -1 corresponds to infinity. Does that mean that seeding can be disabled
using -1, and that it is disabled by default on Galaxy? I don't obtain
exactly the same thing using -1 or 16000 for this parameter, even though the
difference is marginal.
Thanks for your insights
Institut Jacques MONOD
Hi Galaxy team,
I recently met two problems when I used " Fetch sequences> Extract Genomic DNA" in Galaxy Main instance.
I wanted to extract the exons according to the coordinates in a GFF3 file from my reference sequences (from history, and I specified the genome build) which are in FASTA format.
But after checking the output, I found:
1. The first base of each extracted exon was missing in the output, so each extracted exon sequence is one nucleotide shorter than the real length.
2. Some extracted exons are correct,but some extracted exons are wrong. The questionable exons could not be found in the corresponding reference. I can not figure out where they are from.
I tried to read the manual/warnings in the page. But I have no idea with my strange output. Could anyone give me some clues,please?
I would like to visualise by CummeRbund the Cuffdiff results obtained using the cufflinks/cuffdiff workflow on the Galaxy server. My samples include replicates data and when I ask for analysis to be done by CummeRbund, to compare replicates, I get error messages. From past postings I red that the Galaxy Cuffdiff does not allows you to download all the required files to be used by CummeRbund for replicate comparisons. As far as I know, the only way to overcome this problem is to run local computer Cuffdiff. I would like to know if anything has changed so far concerning Galaxy Cuffdiff output files and if there are other options instead of running local computer Cuffdiff to solve this problem.
Any help would be appreciated