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Old 04-23-2008, 11:14 AM   #2
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Location: Sweden

Join Date: Mar 2008
Posts: 324

I am interrested in this also, have you compared quality scores for the misalignad bases at different positions in the reads?

I guess the sequences to use depends on the application, if you are only counting aligned positions (ChIP-seq, transcripome etc) it doesn't matter if the last part is crap as long as the alignment is correct.
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