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Old 08-25-2011, 08:43 AM   #1
idonaldson
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Default BFAST post processing step -a2 or -a3?

I would be interested in hearing which 'algorithm' (-a) flag people use in the 'post processing step' of BFAST (i am using SOLiD data). I have been using '-a3' to include reads that match multiple locations of the reference, but where one match scores better than the rest.

Traditionally i have used only uniquely mapped reads with Corona-Lite (like using '-a2'), but wanted to be more inclusive with the sequenced reads. But i am wondering whether the use of '-a3' is actually a good idea or not.

Any views welcome.

Thank you!
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Old 08-25-2011, 07:19 PM   #2
nilshomer
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Default

Yes, it is the default and gives the best results. You lose a lot in sensitivity if you go to "-a2".
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