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Old 04-25-2011, 06:03 AM   #1
piRWLan
Junior Member
 
Location: Heidelberg

Join Date: Mar 2011
Posts: 1
Default General Question regarding Tophat and Bioscope

Hi everybody,

I have a basic question, which I could not answer so far. I am comparing the alingment strategies of Tophat and Bioscope, and when I got that correct, Bioscopes uses the 5` prime end 25 bp as a seed, in which 2 mismatches are allowed, and is extending it as long as the following alignment does not exceed a certain match/mismatch score.
Tophat is splitting the reads in 25 bp, and is allowing 2 mismatches withing these segments.

So far, so good.. but here is the question.. What does Tophat with the segments, are they glued back together afterwards, or are they treated as indepenend segments throughout the analysis? If they are glued together, is the 2 mismatch limit in every single, or only in the first segment with increasing mismatch limit in the proceding segments to account the higher accuracy in the 5 prime end of the read?

Would be great if someone could help me with this...

Best wishes,

piR
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