[Bioc-sig-seq] a wired problem

[Harris A. Jaffee]

I don't understand where your 'subject1' sequence:

> subject1 = "GTTGGTGCAAACATTAGTTCTTCTGTTGGTGCAACCTTTG"

came from.

Modulo that, everything looks fine.

In my hands, your vcountPattern call finds 41 40-letter elements
of 'seqs', all equal to GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTGAAACAAA,
that match your 41-letter pattern, subject to your

	max.mismatch=1, with.indels=TRUE'

They are all equal to your pattern with its first letter deleted.

I haven't looked closely, but I don't see a reason to doubt this
result.

The following calls would seem to be the sanity checks you want.
They at least confirm the 41 fuzzy matches.

 > countPattern(PCR2rc, "GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTGAAACAAA",
	max.mismatch=1, with.indels=TRUE)
[1] 1

 > matchPattern(PCR2rc, "GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTGAAACAAA",
	max.mismatch=1, with.indels=TRUE)

Views on a 40-letter BString subject
subject: GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTGAAACAAA
views:
     start end width
[1]     1  40    40 [GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTGAAACAAA]

On Sep 28, 2011, at 4:14 PM, wang peter wrote:

> dear all:
>      Using vcountPattern, i found some matched sequences.
> but those are not similar to the pattern.
>      see such coding
>
> rm(list=ls())
> reads <- readFastq(fastqfile);#downloaded from
> http://biocluster.ucr.edu/~tbackman/query.fastq
> seqs <- sread(reads);
> PCR2rc<-DNAString("AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTGAAACAAA")
> result <- vcountPattern(PCR2rc, seqs, max.mismatch=1, min.mismatch=0,
> with.indels=TRUE, algorithm="indels")
> reads <- reads[result]
> seqs <- sread(reads)
> sum(result)
>      then using countPattern, i found they are really not match
>
> subject1 = "GTTGGTGCAAACATTAGTTCTTCTGTTGGTGCAACCTTTG"
> result <- countPattern(PCR2rc, subject1, max.mismatch=1,  
> min.mismatch=0,
> with.indels=TRUE)
> [1] 0
>
> shan gao
>
> 	[[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-sig-sequencing mailing list
> Bioc-sig-sequencing at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing