custom-or-non-default-database

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Juliana Young

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Oct 7, 2021, 3:38:44 PM10/7/21
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Hi Gavin and all,
Hope this finds you guys very well!
I am reaching out because our lab has been using Picrust1-2 in some projects, and now we are interested to run Picrust2 with a custom database for ruminant microbiota. However, we are stacked in the process of creating the custom reference database or default_files/prokaryotic/pro_ref/. I have seen your instructions here https://github.com/picrust/picrust2/wiki/Frequently-Asked-Questions#how-can-i-run-a-custom-or-non-default-database-such-as-the-fungi-18s-and-its-databases, but unfortunately, I still need some more detailed guidance in order to get this done.
Specifically, I would like to ask how to generate the files: pro_ref.hmm, pro_ref.model, pro_ref.raxml_info and pro_ref.tree.
Could you please help me with this? I would appreciate any help!
Thank you very much in advance,
Cheers!
Juliana 

Gavin Douglas

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Oct 8, 2021, 1:41:33 PM10/8/21
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Hey Juliana,

It’s best to creat the tree with RAXML as that will create the model and raxml info files. To get the hmm file you need to run “hmmbuild”, which part of hmmer, on the multiple sequence alignment. RAXML should output a model file if you use that for tree building, but you can also create a model file from an alignment based on the descriptions of the required format here: https://github.com/Pbdas/epa-ng#setting-the-model-parameters

The RAXML info file is trickier, but is only needed for SEPP, which unfortunately is an older format of the file that is output by the current of RAXML. I created the file that is part of the repository manually by editing the RAXML info file I acquired from the output of RAXML to look similar to the input file used in SEPP examples.


Hopefully that helps!

Gavin

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Juliana Young

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Oct 12, 2021, 11:27:03 AM10/12/21
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Hi Gavin, 
Thank you very much for getting back to me so quickly!!! Yup, I will try that and let you know!
Cheers!

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