Entering edit mode
2.5 years ago
Art_SG
▴
10
Hi,
How to map taxonomy assigned using SILVA database to NCBI ID (preferably in R)?
I'm using R Dada2 and SILVA database to assign taxonomy: Bacteria > Firmicutes > Bacilli > Lactobacillales > Enterococcaceae > Enterococcus
I need to map it to NCBI ID: 2 > 1239 > 91061 > 186826 > 81852 > 1350
Or at least use lowest rank to get NCBI ID: Enterococcus > 1350
I see tool such as Crossclasify (and related paper from Monika Balvočiūtė), but DBs over there are quite old (SILVA 128). Any alternative? Is there any map that can be easily used?
Thanks!
Not R but using Entrezdirect:
OR
Thank for that. It is some sort of workaround, but
NCBI has taxonomy dump files available that you can download and the do the mapping locally. Unless the information exists i.e. someone has created that mapping you are not going to find information you are looking for. SILVA is the derived database, NCBI is simply maintaining taxonomy database.
You will generally want to search with just the family/genus names to get a result.