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Trim adapter error #71

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
I hava many reads that have the first 30bp bases of adapter in the 
middle（perfect match），one of reads like 
CGCCACGACGCTCTTCCGATCTCGCCACGACGCTCTTCCGATCTCGCC             
AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC   GTCCGCACATCTCGTAT

adapter is AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC  CTTGTAATCTCGTATGCCGTCTTCTG

the same part is AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC

i use the command is
 cutadapt -b AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCTTGTAATCTCGTATGCCGTCTTCTG -n 2 -O 8  --discard-trimmed -o test1.output --untrimmed-output untrimmed.output3 -f fastq ../R1114.read1.fastq  >&cut3.log

at the end ，the read is not trimmed，I don not known the reason？Can help 
me？

Original issue reported on code.google.com by lufeng89...@gmail.com on 27 Nov 2013 at 9:36

GoogleCodeExporter commented 9 years ago 
Hi, sorry for the late reply. The problem here is that cutadapt tries to match 
the full adapter sequence to the read. The first 34 bases of the adapter match, 
but then the rest doesn't. You can try to give cutadapt a shorter adapter 
sequence, just leave out the last non-matching part.

Original comment by marcel.m...@tu-dortmund.de on 13 Jan 2014 at 7:50

GoogleCodeExporter commented 9 years ago 
Hi:
Thanks for your reply.
I have a question: 
Does not the parameter -o of cutadapt  achieve the aim that using shorter 
adapter sequence.
Waiting for your reply.

lufeng891109

From: cutadapt
Date: 2014-01-13 15:50
To: lufeng891109
Subject: Re: Issue 71 in cutadapt: Trim adapter error

Original comment by lufeng89...@gmail.com on 13 Jan 2014 at 8:17

GoogleCodeExporter commented 9 years ago 
Hi,

no, the -O is just for the minimum overlap. In your example (with -O 8), the 
last eight bases (or more) of the read need to match the first eight bases (or 
more) of the adapter.

Original comment by marcel.m...@tu-dortmund.de on 13 Jan 2014 at 8:48

GoogleCodeExporter commented 9 years ago 
No bug in cutadapt per se.

Original comment by marcel.m...@tu-dortmund.de on 9 Feb 2014 at 10:05

GoogleCodeExporter commented 9 years ago 
Hi,
     Understand what you said,thanks very much.

Original comment by lufeng89...@gmail.com on 13 Feb 2014 at 5:52