Hello
In the example below read2 has 2 mismatches and the adapter was trimmed
correctly. However, read3 has 3 mismatches (and thus is not supposed to be
trimmed) lost its last 3 nucleotides. Can you please help me understand this
issue?
> adapter = "GTAGGCACCA"
> read2 <- DNAStringSet("TGTTGTACCTGTAGGaACaA")
> read3 <- DNAStringSet("TGTTGTACCTGTAaGaACaA")
>
> trimLRPatterns(Rpattern=adapter, subject=read2,
> max.Rmismatch=rep(2,nchar(adapter)))
A DNAStringSet instance of length 1
width seq
[1] 10 TGTTGTACCT
> trimLRPatterns(Rpattern=adapter, subject=read3,
> max.Rmismatch=rep(2,nchar(adapter)))
A DNAStringSet instance of length 1
width seq
[1] 17 TGTTGTACCTGTAAGAA
>
________________________________
From: Harris A. Jaffee <[email protected]>
To: Hongtao Hu <[email protected]>
Cc: [email protected]
Sent: Wed, January 27, 2010 3:40:39 PM
[[elided Yahoo spam]]
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?
[[elided Yahoo spam]]
>
>
> 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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