View Single Post
Old 01-27-2010, 12:46 PM   #5
Nils Homer
nilshomer's Avatar
Location: Boston, MA, USA

Join Date: Nov 2008
Posts: 1,285

Originally Posted by javijevi View Post
Do you mean SAET improved the percentage of bases mapped by BFAST from 55 to 70%? Or are they using another alignment other than BFAST?
I used SAET just now to increase the percentage of bases aligned with BFAST from 55% to 70% at the cost of noise. This was on very old and thus noisy data set so you may get different results. Also, I did not check how this affected detection of polymorphisms (did it correct away the SNPs?). Hence I would not recommend using it until a more conclusive study is performed rather than my one-time anecdotal experience.

"They" (ABI) use mapreads in Bioscope, whereas I use(d) BFAST.
nilshomer is offline   Reply With Quote