[Bioc-sig-seq] ABout how to trim out the adaptor of soleax short data!

Harris A. Jaffee hj at jhu.edu
Thu Jan 28 00:40:39 CET 2010

Patrick's trimLRPatterns function in the Biostrings package.

Beware that the allowed mismatches arguments, including the defaults  
of 0,
are turned into vectors of the same length as the relevant pattern.   
If a
single integer is specified, including the default, it is turned into a
vector with many -1's at the beginning, preventing any partial  
matching of
the pattern.  So, the only possible trimming will be by the whole  
assuming that it matches well enough.  But the presence of the whole  
would be a rare event.  To permit arbitrary partial matching, exact  
or not,
you have to give a vector of the same length as the relevant pattern,  
rep(e, nchar(pattern)), for whatever non-negative e you want to  
allow.  You
can do this separately for the right and left adaptors.

On Jan 27, 2010, at 3:45 PM, Hongtao Hu wrote:

> Hey, dear all,
> The adapotor in our dataset seems variable. Usually, how should it  
> be trimmed out or which software would be used?
> The length of 3' and 5' adapotr are sperately over 20 nt, but the  
> total length of reads is 39 nt.  I wondering if Anyone who ever did  
> the similar job can share your experience? Appreciate!
> Bests,
> Hongtao Hu
> Department of Biological Sicences
> Auburn University
> Auburn, Al 36832
> cell phone: 334-524-7282
> Hongtao webpage: http://www.auburn.edu/~hzh0005/
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