I have some RNA-Seq reads that I want to blast and map to metabolic pathways. Since the RNA-seq results are actually DNA sequence, I used the DIAMOND Blast-Megan5-SEED annotation workflow to achieve what I want. But I am having some issues: 1. I have used diamond to build the reference database using the "protein faa" file of a single bacterial genome from NCBI. 2. I did the diamond blast like this : diamond blastx --sensitive -d nr.dmnd -q 086.fasta -o /086.m8 and I got this result: Total time = 357.682s Reported 27085 pairwise alignments, 27098 HSSPs. 2619 queries aligned. The number of alignment is about right, because i got similar number if I map the reads to the same reference genome using bowtie2, I got similar number. But why is the number of queries aligned so low?
Any input is appreciated, thanks guys!