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Question: Using Megablast to return a Single Hit
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gravatar for nickp60
3.9 years ago by
nickp60 • 0
United States
nickp60 • 0 wrote:

Hello,

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?

 

Thanks!

 

 
megablast galaxy • 705 views
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modified 3.9 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.9 years ago by nickp60 • 0
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gravatar for Jennifer Hillman Jackson
3.9 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

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.

http://usegalaxy.org/u/aun1/p/windshield-splatter

Best, Jen, Galaxy team

 
ADD COMMENT • link written 3.9 years ago by Jennifer Hillman Jackson ♦ 25k
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