How do I download annotation data?

Byron Crump

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Mar 14, 2013, 8:55:55 AM3/14/13

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I used IMG/M to annotate contigs from ten metagenomes, but now I cannot figure out how to download those annotations. I can get 1000 at a time through IMG/MER, but I have over a million genes in each metagenome. I annotated assembled contigs, so there is no information in IMG about the number of DNA fragments for each contig in the original metagenomes. By downloading the annotation data I can put a number on each contig and quantify the relative abundance of genes in the environment I am studying. Can anyone tell me how to download the data? I can do this with MG-RAST, but would prefer to use annotations done in IMG.
Sincerely,
Byron

kl...@lbl.gov

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Mar 14, 2013, 7:08:01 PM3/14/13

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All downloads are currently available from JGI Portal. For example, metagenome http://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=3300000350

There is a link called "JGI Portal" or the Download button, which will redirect you to the JGI Portal http://genome.jgi-psf.org/pages/dynamicOrganismDownload.jsf?organism=UncEn_3300000350

You can search for all the metagenomes you are interested in on the JGI Portal site http://genome.jgi-psf.org/

Ken

Byron Crump

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Mar 15, 2013, 6:11:41 AM3/15/13

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Thank you for the help, but the JGI Portal pages for my private databases do NOT include that convenient Download button or a link called "JGI Portal"
I tried to log in to the JGI Portal site (http://genome.jgi-psf.org/), but it would not accept my login and password
I tried to search for my private databases (that I access through JGI/MER) on this site without logging inbut could not find them.
Please help!
Byron

Manoj Pillay

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Mar 15, 2013, 5:35:18 PM3/15/13

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Byron,

Enabling user access to all IMG data via JGI Portals is actively being worked upon and will be available for most kinds of data in the near future. Please stay tuned for an announcement in this forum. Use your JGI SSO account credentials to log in, into the Portals. But, please wait until the announcement appears here before you try to log in next.

- Manoj

Manoj Pillay

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Apr 26, 2013, 6:47:11 PM4/26/13

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Byron,

Just getting back to you on the status of data downloads. Data should now be available for download for all your IMG Taxons. To learn how to access this, please see the most recent announcement on the forum or click here . Please let me know if you find any issues.

- Manoj

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