Sylvain Mareschal, Ph.D.
Bioinformatics engineer
April 16, 2020 at 20:00
Related entries:
This R package (formerly called MLPA) combines functions to process .fsa files produced by Applied Biosystems' capillary sequencers in the context of RT-MLPA experiments, either to classify samples according to their Gene Expression Profiles (Mareschal, Ruminy et al. JMD 2015) or to identify gene fusions from Sanger sequencing (Mareschal, Palau et al. under review). It can be downloaded on the CRAN website, or installed directly in R with install.packages("FSAtools").

To report bugs, ask questions or get the latest version, please visit the Github repository.

Gene Expression Profiling

Design file for GCB / ABC classification: GCB-ABC_1.9.1.conf
Stand-alone version for Windows: MLPA_1.9.1_install.exe

Either use the stand-alone version or execute GEP.interface() in R after loading the package to summon the graphical interface. Select the design file and the directory storing .fsa files, name an output .log file to determine where to produce PDF and CSV files and click "Process".

R users can try the underlying GEP.process(...) function and various lower level functions for finer control (see examples in R manual pages).

Gene fusions

Requires version 1.10 or newer, no stand-alone available yet.
Please take contact if you need help to build the design data.frame.

No graphical interface is yet available, but multiple .ab1 files can be processed with relative ease using the fusions.process(...) function. Simply provide the path to a directory storing .ab1 files, the design of all possible fusions as a data.frame, a sample sheet describing which files correspond to forward or reverse sequencing and the path to an output directory. Please refer to the corresponding R manual page (?fusions.process) for further details.