Abundance scaled by FMG abundances?
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#84 Abundance scaled by FMG abundances?
Hello,
Any advice for using the abundances for the 40 marker genes as a kind of baseline genomic abundance to correct for IGC gene abundances? I'm thinking of just dividing each IGC abundance by the average of these 40.
Thanks for your help,
Peter Bazeley
I would advise to use the mOTUs and the built in taxonomic pipeline for
taxonomic abundances. I don't see the logic of mixing single gene
abundances and taxonomic abundances.
On Mon, Apr 2, 2018 at 17:30 Peter Bazeley theoark@users.sourceforge.net
wrote:
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Not for taxanomic comparison but as a way to deal with compositional bias. Wouldn't this give a kind of average gene abundane per species, or am I way off?
Hi. So in my quest to find abundances for the FMGs in each sample, it appears that there's no good way to associate COGs with the IGC catalog (or is there?). So the alternative appears to be to take the gene.prediction.assembly result sequences, extract the ones that were matched with the FMGs, and align those to the IGC catalog. Does that sound reasonable? Thanks, Peter
The IGC catalog has been annotated to eggNOG and about 20 other databases,
which makes it possible to summarize gene abundances at all those levels.
And this is done automatically by MOCAT in the functional step. Don't know
what you mean by FMG.
On Fri, Apr 6, 2018 at 00:10 Peter Bazeley theoark@users.sourceforge.net
wrote:
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