Background: to genotype a microsatellite (SSR), one first uses PCR to amplify the given locus, with fluorescent primers. The fragments then migrate through a gel, and a machine records fluorescent intensity through time. The resulting raw data correspond to a chromatogram.
With machines from Applied Biosystem, such raw data are often exported in a binary format (see specification), with the extension .abi
or .fsa
. Such files are readable by the read.abif
function in the R package seqinr.
With machines from Beckman Coulter, raw data are often exported in a set of binary formats named CEQ
(mentioned here), files corresponding to sample data having the .cqs
extension. Unfortunately, it doesn't seem that the format specification is available. But in any case, does someone know how to read such a format in R? (or in any other programming language)
The documentation of the Fragman package (v1.0.7 on CRAN) says : "
storing.inds
is the function in charge of reading the FSA or txt(CQS) files". The expression "txt(CQS)" is not very clear as.cqs
files are not text but binary. Moreover, when looking at the code ofstoring.inds
, we can see that it uses thescan
function to read "txt(CQS)" files, hence assuming they are text.Sorry I can't be of more help. This is not my area. I just happened to know about this package.