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raw-lab / NFixDB

Comprehensive database for diazotroph nitrogenases, alternative nitrogenases, and nitrogenase-like enzymes at the University of North Carolina at Charlotte (UNCC)
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What file do I need? #1

Open freynewton opened 1 month ago

freynewton commented 1 month ago

I am just trying to get my head around the similarities/concurrences of NFixDB and PICRUSt2. I intend to create a dataset of projected/expected expression/abundance of nifH among my soil samples give their 16S sequencing data. Which files should be used as the "functional abundance table (tabular)" for the PICRUSt2 workflow? Is this necessary or can this all be done using NFixDB? Thank you!

raw-lab commented 1 month ago

Good evening Frey,

So, we are a bit unsure by your question. NFixDB is a database of HMMs and sequences based on whole genome analysis which includes nifDHK and their alternatives anf/vnfDHK.

PICRUST2 predicts functions based on 16S sequences. NFixDB doesn't do this.

NFixDB is for searching shotgun metagenomic/metatranscriptomes using hmmer.

It could also be used for designing primers with our other tool DeGenPrime.

If you have nifH amplicon data we have a beta code for that called therion.

Let us know?

Many thanks, RAW lab