Hi I'm using stand alone blastn. I got a strange output with duplicated data. If it were for multiple association with different protein ID it would have not been a problem since it could have had a biological meaning. However, it is not the case. Let me use ProtORG1_1...ProtORG1_N to denote the IDs of the first organisms and ProtORG2_1...ProtORG2_N to denote the IDs of the second one. I have this scenario:
ProtORG1_1 ProtORG2_1 100 ProtORG1_1 ProtORG2_1 0.98 ProtORG1_1 ProtORG2_1 0.80 ProtORG1_1 ProtORG2_1 0.77 ProtORG1_1 ProtORG2_1 0.8
where the third column is the alignment score. How can I eliminate this annoying output since I already used max_target_seqs = 1?
I am using two different isolates of the same parasite I don't know if it can be of any use.