What taxonomy should i use? rbcl gene?

First of all, thank you for the training in the galaxy. it made me learn a lot about bioinformatics and its processing. I am a new user, I have learned from this site for a week. but there are some questions related to this tutorial.

  1. In some tutorials shown the processing of metagenomic data from bacteria, and it uses a taxonomy in the form of “silva” data (silva.v4.fasta). incidentally my research is abaout diversity of “diatom” and primers that I use is rbcl, the question is, what taxonomy do I use in processing data in the galaxy later? rbcl? or other?
  2. if my taxonomy is rbcl, where do I get rbcl.fasta data?

For information, I am waiting for the results of my sample sent by the NGS method, and I can’t wait to process it.

I appreciate your response and looking forward to it :smiley:

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Hello @guardian_cp

This particular analysis domain space (diatom metagenomics) is a bit out of my lane, but this publication seems interesting. The authors host rbcL taxonomic reference databases for both Mothur and DADA-2.

Maybe have a look? And others reading are certainly welcome to comment more!

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Very helpfull, Thanks a lot. Im gonna try this out and reporting the result!

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