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

Florent Angly florent.angly at gmail.com
Tue Mar 9 01:41:33 EST 2010


Hi Juan,
How about you throw away sequences that have a mismatch in the adapter?
After all, if there is a mismatch in the first few bases, it does not 
bode well for the rest of the sequence and there are so many sequences 
that it is not a big loss.
Florent


On 09/03/10 14:50, Juan Jovel wrote:
>
>
> 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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