Question: Raw Data For Soil Metagenomes?
1
gravatar for Pawel Szczesny
6.6 years ago by
Pawel Szczesny3.2k
Poland
Pawel Szczesny3.2k wrote:

Are there any raw data available for whole genome shotgun of soil metagenomes? There are a few studies here and there, but these are mostly 16S rRNA studies, not full sequencing.

I know MGRAST contains a few studies and I stumbled across Terragenome initiative, however the former doesn't always provide raw data, and the latter doesn't seem to provide any data at all.

EDIT: To make things clear: I'm looking for raw data of systematically defined "soil" metagenomes (some rhizosphere metagenomes qualify as well).

metagenomics next-gen • 2.7k views
ADD COMMENTlink modified 22 months ago by Biostar ♦♦ 20 • written 6.6 years ago by Pawel Szczesny3.2k
2
gravatar for Mary
6.6 years ago by
Mary11k
Boston MA area
Mary11k wrote:

Have you tried IMG/M for leads? http://img.jgi.doe.gov/cgi-bin/m/main.cgi

EDIT to note: I just realized this little note on there might not be seen by some folks until tomorrow, when it will be too late....

All IMG systems will be down Tue. June 26, 2012 for maintenance. Sorry for the inconvenience.

ADD COMMENTlink modified 6.6 years ago • written 6.6 years ago by Mary11k

Thanks - very good pointer. Metadata sorting (ecosystem subtype and minimal level of protein coding genes) quickly got me required data.

ADD REPLYlink written 6.6 years ago by Pawel Szczesny3.2k
1
gravatar for Cliff Beall
6.6 years ago by
Cliff Beall450
Ohio
Cliff Beall450 wrote:

http://www.ncbi.nlm.nih.gov/sra?term=soil%20metagenome gives 619 hits, it looks like many of them are shotgun sequences.

ADD COMMENTlink written 6.6 years ago by Cliff Beall450

I wasn't clear in the original question. I'm looking for some more systematic classification of soil metagenomes (MGRAST has one, GOLD has one as well), instead of not-so-precise description of the study. But thanks anyway.

ADD REPLYlink written 6.6 years ago by Pawel Szczesny3.2k
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