Hello
In the example below, Rpattern2 (2 mismatches) trims the subject correctly,
while Rpattern3 (3 mismatches) which is not supposed to do any trimming, it
trims the last 2 nucleotides. Can you explain why?
> subject <- DNAStringSet("GCTGGAACCCAGGGTGTTGTACCTGTAGGCACCA")
> Rpattern2 <- "CTGaAGGCACgA" # 2 mismatches
> Rpattern3 <- "tTGaAGGCACgA" # 3 mismatches
> trimLRPatterns(Rpattern = Rpattern2, subject = subject, max.Rmismatch =
> rep(2, 12))
A DNAStringSet instance of length 1
width seq
[1] 22 GCTGGAACCCAGGGTGTTGTAC
> trimLRPatterns(Rpattern = Rpattern3, subject = subject, max.Rmismatch =
> rep(2, 12))
A DNAStringSet instance of length 1
width seq
[1] 32 GCTGGAACCCAGGGTGTTGTACCTGTAGGCAC
> sessionInfo()
R version 2.10.0 alpha (2009-10-01 r49909)
x86_64-apple-darwin9.8.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] rtracklayer_1.5.17 RCurl_1.2-0 bitops_1.0-4.1 ShortRead_1.3.36
[5] lattice_0.17-25 BSgenome_1.13.16 Biostrings_2.13.48 IRanges_1.3.87
loaded via a namespace (and not attached):
[1] Biobase_2.5.8 grid_2.10.0 hwriter_1.1 tools_2.10.0 XML_2.6-0
>
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