Comparing metagenome profiles with publicly available profiles from sandpiper

[adityabandla]

Dear Ben,

I am interested in comparing my metagenomes to a number of samples from the same biome that are publicly available. My comparison would be in the form of beta diversity estimates and the approach would be to (i) pick a subset of markers, (ii) combine otu tables from my metagenomes with the ones from sandpiper, and (iii) calculate beta diversity and check for concordance among markers. Would this approach be valid?

Regards, Adi

[wwood]

Hi,
This seems reasonable. One thing to watch for is that only some of the markers target both Bacteria and Archaea - it might be best to stick to these ones. You can tell which is which using singlem metapackage --describe.

[sheaster]

Hi,
would using the taxonomic profiles rather than otu tables also be valid?
Thanks,
Shea

[wwood]

Hi @sheaster apologies for the very slow response here.

I would say that is only recommended when the community is well represented in genome databases, otherwise you risk having substantial coverage assigned to whole genera, when they might be multiple species present, if you follow?