My goal is to align my metagenomic sequences with virulence gene database in order to find out which probable genes are prevalent in the data.
So I ran diamond aligner using following commands:
1. diamond blastx -d nr.dmnd -q /home/DB04.fasta -o DB04_VG4 --evalue 0.00001 --id 25 --sensitive
2.diamond blastx -d nr.dmnd -q /home/DB04.fasta -o DB04_VG4 --evalue 0.001 --id 25 --sensitive
3.diamond blastx -d nr.dmnd -q /home/DB04.fasta -o DB04_VG4 --evalue 0.001 --id 25 --sensitive --query cover 40
4. diamond blastx -d nr.dmnd -q /home/DB04.fasta -o DB04_VG4 --evalue 0.001 --id 25 --sensitive --subject-cover 40
and few others.
Ofcourse, I am getting different numbers of genes with each command that I have used.
So I was just wondering which is the most reliable in predicting correct ones?
--sensitive is added due to long read sequencing
Or do I need to add some more parameters?
#bioinformatics #metagenomics #diamondalignment