I have this doubt about retrieving best hit from the blast tabular output. Based on the aim I retrieve top hit by filtering the output in excel on the basis of gaps, mismatch, query coverage, etc. Now I saw that the raw output is already arranged in the order of sequence similarity i.e the 1st entry is the top hit for each query. So what if we just remove duplicates from the tabular output in excel. Like this only the first entry for each query will be left which should be the top hit. I want to know if this is correct or not. Is removing duplicates enough.
*ignore those queries which map at multiple locations on a single subject for a time being.