Arabidopsis Thaliana Genome

Question: Arabidopsis Thaliana Genome

6.6 years ago by

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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modified 6.6 years ago by Jennifer Hillman Jackson ♦ 25k • written 6.6 years ago by Franziska Turck • 10

6.6 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

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 -- Jennifer Jackson http://galaxyproject.org

ADD COMMENT • link written 6.6 years ago by Jennifer Hillman Jackson ♦ 25k

6.6 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k 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 -- Jennifer Jackson http://galaxyproject.org

ADD COMMENT • link written 6.6 years ago by Jennifer Hillman Jackson ♦ 25k

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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

ADD REPLY • link written 6.6 years ago by Matthew McCormack • 60

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