6.2 years ago by
To understand what the data looks like in AB1 file, you will want to refer to http://www6.appliedbiosystems.com/support/software_community/ABIF_File_Format.pdf
If you are comfortable in R, you might reach for http://bioconductor.org/packages/release/bioc/html/sangerseqR.html and work with data from calling peakAmpMatrix (or traceMatrix)
Or, in perl, then, http://search.cpan.org/~vita/Bio-Trace-ABIF-1.05/lib/Bio/Trace/ABIF.pm
However, the specifics of what you want to compute are not entirely clear to me.
Making reference to the vignette http://bioconductor.org/packages/release/bioc/vignettes/sangerseqR/inst/doc/sangerseq_walkthrough.pdf, given these definitions
P1AM.1 Amplitude of primary basecall peaks.
P2AM.1 (optional) Amplitude of the secondary basecall peaks.
Then "the ratio of the peak value of nucleotide with the strongest signal at one position to the peak value of the nucleotide with the second strongest signal" is simply P1AM.1 / P2AM.1, which can be computed for demo AB1 file as follows:
> x <- read.abif(system.file("extdata", "heterozygous.ab1", package = "sangerseqR"))
> x@data$P1AM.1 / x@data$P2AM.1
Note however that this is the value is ratio of peaks. Not area under the peak. It is usually greater than one but not always. You may want to reconsider exactly what you are trying to determine. Good luck.