is there a way to know #unaligned reads when using diamond blastx?

lapi

New member
Hi all,

I was using command
diamond blastx --query xxx.fq.gz --db nr.dmnd --daa xxx.daa and get an output like this:
...
...
Closing the database file... [0.011s]
Deallocating taxonomy... [0s]
Total time = 3408.63s
Reported 5507204 pairwise alignments, 5507443 HSPs.
281370 queries aligned.

I understood 281370 reads were aligned to the protein database. What do the number 5507204 and 5507443 mean?
Also, is there a easy way that diamond can report the number of unaligned reads?

Thanks a lot in advance,
Yun
 

Benjamin Buchfink

Administrator
Staff member
It is the number of alignments reported. For one target there will be up to 25 alignments reported, by default. The second number also counts multiple alignments between the same query and target.

There is no option to report the number of unaligned reads at the moment.
 

lapi

New member
It is the number of alignments reported. For one target there will be up to 25 alignments reported, by default. The second number also counts multiple alignments between the same query and target.

There is no option to report the number of unaligned reads at the moment.
Hi Benjamin,

thanks for the reply! Then I just do the maths: #unaligned reads = #total reads - #queries aligned. That should be fair, right?
 
Top