Hello, I have some metagenomic contigs and I want to use blastn against Silva SSU and LSU database to get taxa information.
I download the Silva RDP database from here in fasta format
I try to use blastn to blast it directly. However, it doesn't work. Someone told me I have to convert it to NCBI format, but I don't know how to do it.
Also, the Silva database sequences are RNA seqs. I think I need to convert it to DNA first. I don't know how to do it.
I know after I convert it to DNA seqs, I can use "makeblastdb" to convert make the database. However, I don't know how to set "makeblastdb" parameters.
Can anyone help me. Post the scripts I should use.
Thanks,
Ben
I download the Silva RDP database from here in fasta format
I try to use blastn to blast it directly. However, it doesn't work. Someone told me I have to convert it to NCBI format, but I don't know how to do it.
Also, the Silva database sequences are RNA seqs. I think I need to convert it to DNA first. I don't know how to do it.
I know after I convert it to DNA seqs, I can use "makeblastdb" to convert make the database. However, I don't know how to set "makeblastdb" parameters.
Can anyone help me. Post the scripts I should use.
Thanks,
Ben
Comment