Arabidopsis thaliana genome
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
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
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Jackson http://galaxyproject.org
participants (2)
-
Franziska Turck -
Jennifer Jackson