use R to read CQS file (chromatogram format from Beckman Coulter)

Question

[Timothée Flutre]

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)

Answer 1

[Jean-Karim Heriche]

I think the Fragman package can read these files.

[Timothée Flutre]

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 of storing.inds, we can see that it uses the scan function to read "txt(CQS)" files, hence assuming they are text.

[Jean-Karim Heriche]

Sorry I can't be of more help. This is not my area. I just happened to know about this package.