Hey guys,
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!
Why do you think the number of queries aligned is so low?
Because in 27085 pairwise alignments, 2619 queries aligned. In other people`s post, these two numbers are similar. And since I got ~27000 reads mapped to the genome (bowtie2) I would expect similar numbers in diamond blast, right?