While Arabidopsis lyrata is listed under 'A', you will find Arabidopsis Columbia is often listed under 'M' for Mouse Ear Cress on the drop-down lists of genomes found in Galaxy. They are near the mouse genomes. Both TAIR9 and TAIR10 are available.
Matthew
On 4/26/2012 12:55 AM, Jennifer Jackson wrote:
Hi Franziska,
Both species are available for NGS mapping tools (excluding megablast, which is not intended to host individual genomes on the public instance). To locate these, including /A. thaliana/, type in 'Arab' into the "Select a reference genome:" box to perform a search. Perhaps default sort order of the builds list when viewed by scrolling is what made it appear that only /A. lyrata/ was available (it is the first in the list and has a different legacy name structure)?
Many people use the main public instance to do NGS mapping every day. There are significant resources dedicated to this service, but there are usage quotas, limits on job size (72 hr job runtime limit), and delays during peak usage times (we are experiencing one right now). Your needs will determine the best type of Galaxy instance for your purposes.
This wiki has details about Galaxy options: http://wiki.g2.bx.psu.edu/Big%20Picture/Choices
Hopefully this helps,
Jen Galaxy team
On 4/25/12 2:02 PM, Franziska Turck wrote:
Dear Jennifer,
actually I wanted it for NGS mapping and it wasn`t in the drop down menue although Arabidopsis lyrata was. Is NGS mapping with GALAXY even realistic or does it take too much cpu time on the cluster.
Best, Franziska
----- Original Message ----- From: Jennifer Jackson jen@bx.psu.edu Date: Wednesday, April 25, 2012 22:46 Subject: Re: [galaxy-user] Arabidopsis thaliana genome To: Franziska Turck turck@mpipz.mpg.de Cc: galaxy-user@bx.psu.edu
Hello Franziska,
TAIR9 and TAIR10 are available for most tools, with the notable exception of the new 'NGS: GATK Tools (beta)' tool set. Is this where you wanted to have the genomes added? For now, only one genome is available while in beta and using the custom reference genome feature for other genomes is the current option.
Our plans are to add genomes to the GATK tool set and fill in genomes for other tools in the near term. I can make sure that the Arabidopsis genome is included. Normally, we would put as a priority the most current build, which would be TAIR10. Are other builds of interest? Links and other information would be great. The source we have used in the past is (below), please send additions/corrections, help is always appreciated! The core input is a fasta version of the genome, with additional related data such as Mitochrondrial, Chloroplast, Plasmid, etc. as appropriate. ftp://ftp.arabidopsis.org/home/tair/Sequences/whole_chromosomes/
Until this is completed, here are instructions for using a custom reference genome (available with most tools): http://wiki.g2.bx.psu.edu/Support#Custom_reference_genome
Best,
Jen Galaxy team
On 4/25/12 8:06 AM, Franziska Turck wrote:
Dear Galaxy team!
Could you put the Arabidopsis thaliana genome in the drop down list? What kind of data would you need for that, I can help find all
the links
from TAIR
Best, Franziska
Dr. Franziska Turck Max Planck Institute for Plant Breeding Research Department Plant Developmental Biology Group Transcription Control by Chromatin Structure
Carl von Linné Weg 10 50829 Köln Germany
Tel: +49 221 5062 246 Fax:+49 221 5062 207
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Dr. Franziska Turck Max Planck Institute for Plant Breeding Research Department Plant Developmental Biology Group Transcription Control by Chromatin Structure
Carl von Linné Weg 10 50829 Köln Germany
Tel: +49 221 5062 246 Fax:+49 221 5062 207
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