Question: DIAMOND BLAST less queries aligned than reported alignment
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gravatar for dazhudou1122
4.2 years ago by
dazhudou1122110
dazhudou1122110 wrote:

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!

sequencing rna-seq alignment • 1.7k views
ADD COMMENTlink written 4.2 years ago by dazhudou1122110

Why do you think the number of queries aligned is so low?

ADD REPLYlink modified 4.2 years ago • written 4.2 years ago by biotech540

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?

ADD REPLYlink written 4.2 years ago by dazhudou1122110
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