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

Noll, Aaron acn at stowers.org
Tue Mar 9 01:31:49 EST 2010


http://hannonlab.cshl.edu/fastx_toolkit/commandline.html

try out the clipper tool

FASTA/Q Clipper

        $ fastx_clipper -h
        usage: fastx_clipper [-h] [-a ADAPTER] [-D] [-l N] [-n] [-d N] [-c] [-C] [-o] [-v] [-z] [-i INFILE] [-o OUTFILE]

        version 0.0.6
           [-h]         = This helpful help screen.
           [-a ADAPTER] = ADAPTER string. default is CCTTAAGG (dummy adapter).
           [-l N]       = discard sequences shorter than N nucleotides. default is 5.
           [-d N]       = Keep the adapter and N bases after it.
                          (using '-d 0' is the same as not using '-d' at all. which is the default).
           [-c]         = Discard non-clipped sequences (i.e. - keep only sequences which contained the adapter).
           [-C]         = Discard clipped sequences (i.e. - keep only sequences which did not contained the adapter).
           [-k]         = Report Adapter-Only sequences.
           [-n]         = keep sequences with unknown (N) nucleotides. default is to discard such sequences.
           [-v]         = Verbose - report number of sequences.
                          If [-o] is specified,  report will be printed to STDOUT.
                          If [-o] is not specified (and output goes to STDOUT),
                          report will be printed to STDERR.
           [-z]         = Compress output with GZIP.
           [-D]         = DEBUG output.
           [-i INFILE]  = FASTA/Q input file. default is STDIN.
           [-o OUTFILE] = FASTA/Q output file. default is STDOUT.

This is a suite of nice utilities that can be downloaded and that by the way are also used by galaxy.

-Aaron

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Juan Jovel
Sent: Monday, March 08, 2010 10:51 PM
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!

 JUAN


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