Songbird for cross-kingdom comparisons?

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1

Hi!

Was wondering if it would be correct to apply the differential ranking concept to directly compare 16S with ITS if one uses known reference standards in both datasets. I realize Songbird does not normally require internal controls (e.g. reference spikes). But if one introduces control DNAs for both bacteria and fungi in the samples prior to extraction and amplicon generation and uses those in the DR analysis, in theory that may allow to do DR across the two types of datasets (16S and ITS)? Or not ?

Thank you!

Mircea

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Hi, yes spike-ins can help with cross 16S / ITS comparisons, as long as you have spike-ins for both datasets. You can run differential abundance independently for 16S, ITS and use the spike-in to correct for the absolute abundance bias.

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