I work with metagenomic and metatranscriptomic data. I know the nt/nr database is for nucleotide reads which my data is all in nucleotide form (not in protein form so I wouldn't be using blastp). But when I do a local blast, I am just wondering how to know if I should use nt or nr. Because with blastp, you only use nr for protein nucleotide sequences. If I have metatranscrptomic reads, I did use blastn against the nt database and I got a lot of hits so I felt that was okay.
When I use FragGeneScan to extract protein reads from the RNA sequences I did use nr database and just wondering if this makes sense or should I have used the nr database from the start?
I've read a lot on this on NCBI but it is very clear to me in practise.