3.9 years ago by
Raising the coverage/id threshold can often seem like a simple solution to achieve this end, but are actually not the best path. "Top hit" is a bit complicated, especially when the query is a bit sticky (attracts many common hits, due to the properties of the content in the target reference database). But there are most certainly solutions!
A prior publication from our team contains a great deal of method detail and live resource (including best practices for post-filtering megablast results into usable results). Please review and see what is useful for you. The workflow example can be imported into your account and tuned any way that you wish.
Best, Jen, Galaxy team