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
pattern,
assuming that it matches well enough. But the presence of the whole
adaptor
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,
e.g.
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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