Sylvain Mareschal, Ph.D.
Bioinformatics postdoc
May 15, 2016 at 16:50
MLPA 1.9.1
Related entries:
This software was developed to handle .fsa files produced by Applied Biosystems' capillary sequencers in the context of RT-MLPA experiments. Provided a proper configuration file, it normalizes signal, infers peak dimensions and computes GCB / ABC probabilities. It was extensively tested on a 3130 Genetic Analyzer, however it should be compatible with any sequencer outputting FSA files.

License
This software is released under the terms of the GNU Public License 3, fully available within the distributed packages.

Design file
GCB/ABC classification: GCB-ABC_1.9.1.conf

Stand-alone version
Windows XP and above: MLPA_1.9.1_install.exe
Windows users not familiar with the R language should use this version. Simply follow the installer and launch the software, select the FSA files to process, the design file (see above) and the output directory. The output directory should contain a PDF file with profiles, many TSV files (to be read with Excel or similar software) and a LOG file with messages and warnings.

R package
R source package: MLPA_1.9.1.tar.gz
R binary package: MLPA_1.9.1.zip
The software described here relies on a R package, that can be installed and used as any other R library. The R software must be installed first on your machine (freely available on most platforms, see the official website). Once the library installed in R, the interactive interface on which the stand-alone version relies may be summoned using the MLPA.interface() command, or similar processing may be achieved in command line with the MLPA.process(...) function. Lower level classes and functions are finally accessible to browse and process data, please refer to the library documentation for further details.

# Installation and loading
install.packages("MLPA_1.9.1.tar.gz", type="source")
library(MLPA)

# Interactive interface
MLPA.interface()

# Command line interface
MLPA.process(
  input = c("file1.fsa", "file2.fsa"),
  design = "design.conf",
  output = "output/"
)