blastx -strand option

[pkaruso0]

blastx has a -strand plus/minus option. can this be implemented in diamond blastx? The reason I ask is that I have error prone nanopore data from large amplicon libraries, I can use cutadapt to search for the PCR primer and the reverse complement so that the cutadapt output file is now only positive strands. Any strands that are not positive were in the vector backwards and would be filtered out with "blastx -strand plus"

[bbuchfink]

Yes, I will consider this for the next release. For now you can filter these hits from the output file.

[pkaruso0]

great. Look forward to that. In the meantime, how would I filter out reads that were in backwards?

[bbuchfink]

You can check for the query start position being larger than the query end position. There's also the qframe output field.