RDP and Green genes classification issues

Feature requests
1

Dear Mothur,

I was trying three taxonomic databases for classification. I realised that there is big difference between RDP and greengenes when it comes with Proteobacteria and cyanobaceria
Order Ys2 is Proteobacteria in RDP whereas its Vampirovibrio from Cyanobacteria in GreenGenes.
In this case would rather prefer more true phylum to be assigned to sequences and I am not sure which one correct.

So I would like to merge these green and RDP databases for mothur classification.
In this case I would rather prefer more true phylum to be assigned to sequences and I am not sure which one correct.

looking forward for reply!!

2

That is a hornets nest. The reason there are more than three taxonomies out there is because no one can agree. You are certainly free to make your own taxonomy and reference files. I’d suggest possibly talking with the folks at the RDP, greengenes, and SILVA about what might be going on with this group. It’s not really a mothur issue, rather it’s a database issue.

3

Hello Pat,

Thanks for your reply!
Can you give me an idea how can i make my own reference. which later can be used in mothur.

4

I’d suggest just modeling whatever you do after the other taxonomies - no spaces in taxonomies, separate each level with a semicolon, end each line with a semicolon, same sequence names in the fasta and taxonomy file. those should get you going…

5

Thank you Pat!!!

6

So I would like to merge these green and RDP databases for mothur classification.
In this case I would rather prefer more true phylum to be assigned to sequences and I am not sure which one correct.

7

You can’t merge the taxonomies. Just use both for the classifications and see what you get.