The orientation of primer sequences

[nmgduan]

Hello,

I want to ask if I trian my own classifier.

Should the orientation of forward and reverse sequences which are the input of --p-f-primer and --p-r-primer be 5' → 3‘?

Thanks in advance!

Sarah

[Nicholas_Bokulich]

It does not matter, so long as the reads are all in the same orientation.

Similarly, the query sequences do not need to be in the same orientation as the reference sequences, as long as they are not in mixed orientations.