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

michael watson (IAH-C) michael.watson at bbsrc.ac.uk
Tue Mar 9 01:38:26 EST 2010

Use fastx toolkit or something within emboss.  Failing that, just write something in pure perl:) 
From: bioperl-l-bounces at lists.open-bio.org [bioperl-l-bounces at lists.open-bio.org] On Behalf Of Juan Jovel [jovel_juan at hotmail.com]
Sent: 09 March 2010 04:50
To: bioperl
Subject: [Bioperl-l] How to trim 3' adaptors from solexa reads?

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!


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