Hi Guys,

I have Bowtied (aligned) sequences against a local database having few sequences 
of length between 70-300bp. Now lets take SeqA  of length 120bp from my target 
database. Since the RNA-Seq reads are of length 38bp i guess, how do i ascertain 
that for instance 3 different reads aligned perfectly to cover the SeqA.  


many thanks in advance,
Chu


      
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