It is imy first time to use Mothur!
I searched for the taxonomy file for Silva database :
but unfortunately I couldn’t find it.
the tax files in:
are different in IDs than those in the first link.
Could any one help me?
The “SILVA database” that we talk about is what you found in the Silva_reference_files link.
Thank you for the reply.
I is it posible to create a taxonomy file by my own, if the taxonomy exist in the header of a fasta file?
for example, I have a fasta file whose header is like that:
AAAA02045240.678.2192 Bacteria;Bacteroidetes;Flavobacteria;Flavobacteriales;Flavobacteriaceae;Flavobacterium;Oryza sativa Indica Group
AGAGUUUGAU CCUGGCUCAG GAUGAACGCU AGCGGCAGGC CUAAUACAUG CAAGUCGGAC GGGAUCCGUC GGAGAGCUUG
CUCGAAGACG GUGAGAGUGG CGCACGGGUG CGUAACGCGU GAGCAACCUA CCUCUAUCAG GGGGAUAGCC UCUCGAAAGA
I tried to remove “>” and add “;” at the end of the line to be like the taxonomy format you have, but it gives me error saying:
‘AAAA02045240.678.2192’ is in your template file and is not in your taxonomy file. Please correct.
Your help is appreciated!
Sure but there are some rules…
- No spaces in the taxonomy. You might replace them with “_”
- The taxonomy string needs to have a “;” at the end.
- The SILVA sequences have spaces in them between groups of 10 bases - remove those too.
I suggest to add sort option (for p-value) and cutoff (otu pairs higher than 0.05 p-value can be discarded) for otu.association command. I have over 1500 otus and the list is quite long, so it is hard to manually sort it.
Ok - but can’t you sort it in R, excel, command line, etc?