recommended taxonomy for Silva 18S

[Colin Brislawn]

Good afternoon,

I'm planning on using Silva 119 to assign taxonomy to 18S data. I wanted to check in on the recommended taxonomic annotations.

I play to use this sequence file:

/Silva119_release/rep_set_eukaryotes/97/Silva_119_rep_set97_18S.fna

What matching taxonomic file would you suggest?

/Silva119_release/taxonomy_eukaryotes/97/taxonomy_97_7_levels_18S.txt 

/consensus_majority_taxonomy_SILVA119/consensus_taxonomy_eukaryotes/97/taxonomy_97_7_levels_consensus.txt

/consensus_majority_taxonomy_SILVA119/majority_taxonomy_eukaryotes/97/taxonomy_97_7_levels_majority.txt

Thank you for the input.

Also, if there is any other things I should consider when working with 18S data, please let me know.

I appreciate the advice,

Colin Brislawn

[TonyWalters]

The /Silva119_release/taxonomy_eukaryotes/97/taxonomy_97_7_levels_18S.txt file is the taxonomy that is pulled directly from the representative sequence for that OTU. The majority file matches taxonomy from all sequences in the OTU, and if a taxa string for a given level is less than 90% for a given level, it becomes unclassified. The consensus taxonomy file requires 100% match across all sequences in the OTU, or the taxonomy becomes ambiguous. So the taxonomy should be more assured for the majority/consensus taxonomy at the potential cost of having less depth.

There are not hard and fast rules as to which to go with, but I would suggest going with the majority taxonomy.

[Colin Brislawn]

I would suggest going with the majority taxonomy.

Thanks Tony. Thanks exactly the kind of recommendation I was looking for. 

I really appreciate you manually curating this database, and providing documentation on how you did it, and providing support and commentary long after it's release. This is a huge contribution and I greatly appreciate it.

Thanks for everything Tony,

Colin Brislawn