[Bioperl-l] How to trim 3' adaptors from solexa reads?

[Juan Jovel]

Hello Guys!
 
Does anybody has a good suggestion on how to trim 3' adapters from reads coming out from the Illumina pipeline?  It becomes specially difficult when the quality of the reads is poor at the 3' end.
 
I have been doing that with BioConductor (ShortRead library), but still is not good enough to fish adapters that contain mismatches in the Solexa reads.
 
 Any suggestion will be appreciated.  Thanks!
 
 JUAN
 
 		 	   		  
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