I’m new for using DIAMOND and MEGAN. I already run the alignment for my samples using DIAMOND, but the result is reducing almost 25%. I have only get 75-80% queries aligned with DIAMOND? Is it still good to perform it in MEGAN?
I also get a .daa file from the alignment, but i wonder how much file i should get when i perform 4 samples? In my case, i only get one .daa file from 4 samples.
Here is command that i used for perform the alignment:
diamond blastx -d nr -q HA_result/final.contigs.fa -o matches.daa
diamond blastx -d nr -q HB_result/final.contigs.fa -o matches.daa
diamond blastx -d nr -q IA_result/final.contigs.fa -o matches.daa
diamond blastx -d nr -q IB_result/final.contigs.fa -o matches.daa
Thank you so much.