[BioC] A problem about trimLRPatterns

[Harris A. Jaffee]

I'm not sure what you are doing.  Let's change your "A" to "C", so we don't
confuse it with the lower case a's.  Then we have this example, which looks
ok to me since the "C" is not trimmed.  

pattern = "TCGACTG"
subject = "aaaaaaCTCGACTG"
trimLRPatterns(subject=subject, Rpattern=pattern, with.Rindels=TRUE, max.Rmismatch=1)
[1] "aaaaaaC"

What happens to you?  Please be explicit.

On Mar 1, 2012, at 4:05 PM, wang peter wrote:

> i have found a problem
> if we allow edit distance as 1, with indel=1
> subject aaaaaaATCGACTG
> pattern                TCGACTG
> and i found some reads were trimmed ATCGACTG
> not TCGACTG
> 
> that is ok for RNA-seq
> but not ok for microRNA, if we want to keep the whole microRNA sequences
> 
> -- 
> shan gao
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