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merenlab / merenlab.org

Web content for Meren Lab
http://merenlab.org
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Adding two new posts to the website #136

Closed ivagljiva closed 3 years ago

ivagljiva commented 3 years ago

This PR merges two new posts associated with our upcoming anvi'o release (v7.1).

The first one is the nif MAG blog post, scheduled for publication on 10/20/2021. It discusses how to use anvi-estimate-metabolism to perform targeted binning of a metabolically-interesting population.

The second one is a mini-tutorial on running metabolism estimation and metabolic enrichment analyses, based upon the FMT study. It is scheduled for publication on 10/22/2021.

@meren, I consider both of these posts to be publication-ready, but please feel free to look them over and make edits (or tell me to make them) as you deem necessary. :)

In addition, I suggest that we add a link in the FMT study reproducible workflow connecting it to the enrichment analysis in the second post. It will provide an explanation as to how we obtained our "modules of interest" in the metabolic completion section. Let me know what you think :)

Thanks to everyone who helped me edit these posts, particularly @meren, @efogarty11 , and @mschecht!

meren commented 3 years ago

Read and reproduced. Great stuff, Iva. Thank you very much.

For the metabolism mini-tutorial I would probably have started with a single FASTA file, turn that into a contigs db, run anvi-run-kegg-metabolism on it, then run anvi-estimate-metabolism on it to show that it really does estimate metabolisms, saying you can learn much more here about ways to run it (but since this will be the first time people will be seeing this, I would go through a few examples, giving time to people to appreciate this).

But how can we do comparative genomics with a focus on metabolic potential across many genomes? "here I have many contigs dbs for you from one of our recent studies, so I will let you download that one to play with (and if you can't download it in 2 seconds, YOU. ARE. OUT microphone feedback noises" (because radiating unyielding authority in a workshop always keeps everyone awake).

My 2 cents.

ivagljiva commented 3 years ago

I took your advice and added an initial section covering the steps for a single genome :)

Feel free to take a look and merge this if you feel it is good to go.

meren commented 3 years ago

I took your advice and added an initial section covering the steps for a single genome :)

you are the best, Iva. this is great.

I will merge it after fixing a little conflict here.