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BenKaehler / readytowear

Ready-made Taxonomic Weights Repository
BSD 3-Clause "New" or "Revised" License
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Asking about animal-proximal-gut.qza #24

Open khb3850 opened 1 year ago

khb3850 commented 1 year ago

Hello, I'm Hanbeen Kim.

Thank you for being so dedicated.

I have a question about "animal-proximal-gut" database.

I have studied the rumen microbiome and tried to make a weighted classifier.

Does the "animal-proximal-gut" mean rumen?

If it is not, can you advise how to make a specific database to make a weighted classifier?

I hope you have a nice day.

Hanbeen Kim.

BenKaehler commented 1 year ago

Thanks @khb3850!

The EMPO3 Animal Proximal Gut habitat includes gut intestine, gizzard, crop, lumen, and mucosa, as examples. Those examples are taken from here. So it might be appropriate for rumen. You could try the animal-proximal-gut and the average weight pretrained classifiers to see how they affect your results.

If you have a few hundred of your own lumen samples, you could use them to train your own weighted classifier using q2-clawback. There is a tutorial if you want more details on that process.

Hope that helps!