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Old 01-27-2010, 11:11 AM   #2
nilshomer
Nils Homer
 
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Location: Boston, MA, USA

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Quote:
Originally Posted by javijevi View Post
Hi all,

According BFAST paper(s), this tool is capable of managing read errors in color space of SOLiD data.

Does anybody knows if it is also convenient to clean/correct/purge raw data with accuracy enhancement tools (like SAET) prior to use BFAST? Or maybe is it not wise to do it in order to not alter the BFAST behavior?

I've read that it is highly convenient to use SAET (or similar tool) to improve the quality of data prior to use align/assembly tools, but maybe this recommendation is prior to development of BFAST.

Any experience?

Thanks in advance.
I do not know how SAET works. I would recommend not using SAET and letting BFAST (I am the author) identify color errors versus variants. If you have a recent run with a known reference you can try with and without SAET to assess the difference in color/base error rates after alignment with BFAST. Please PM me if this is the case, since I would interested in the results.

Nils

Last edited by nilshomer; 01-27-2010 at 11:13 AM.
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