Question: Using Megablast to return a Single Hit
gravatar for nickp60
3.9 years ago by
United States
nickp600 wrote:


I am trying to use Megablast in Galaxy to search a file full of environmental 16s samples using megablast.  However, this returns a large number of the closest hits, so that my query file of ~1500 sequences turned into a ~300,000 sequence result.  Is there a way, either directly through the search of by filtering, to have the search return a single hit?





megablast galaxy • 705 views
ADD COMMENTlink modified 3.9 years ago by Jennifer Hillman Jackson25k • written 3.9 years ago by nickp600
gravatar for Jennifer Hillman Jackson
3.9 years ago by
United States
Jennifer Hillman Jackson25k wrote:


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


ADD COMMENTlink written 3.9 years ago by Jennifer Hillman Jackson25k
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