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Old 07-02-2012, 01:17 AM   #1
pinki999
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Location: Germany

Join Date: Oct 2010
Posts: 37
Default How does TopHat deal with poor quality bases?

Hi,

I have a naive question with respect to TopHat. How does TopHat deal with bases with poor quality? Say if there is a 2x75bp reads and only the read2 has few poor quality bases at the end, Are these bases clipped while mapping? and how does that affect the mapping quality?

Any help would be appreciated.

Thank you
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