Hi,

I have some reads with 25 bp adapter at the five prime end. Some of the reads do not have perfect match with the adapter, even with some indels.  I tried to use trimLRPatterns to trim them off, but I got confused with the max.Lmismatch parameter, as it is doing sub-string trimming too. The adapter in my reads are  the full length of 25 bp, without shortening to any substring. How should I specify the parameter then? Or maybe I could use some other functions from ShortRead? Please help. Thanks.

-Kunbin

code I used, but this code cannot accommodate the mismatches.

reads<-readFastq("test.fq")
adapter<-DNAString("CTGGCCTTTGAGACTGGCCCACCTC")
seqs<-sread(reads)
trimCoordsAR<-trimLRPatterns(Lpattern=adapter, subject=seqs, max.Lmismatch =1, ranges=T)

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