T-RFLP identification of ospC

peaksThis code facilitates identification of ospC genotypes from terminal restriction fragment length polymorphism analysis of B. burgdorferi samples (Tsao et al 2013). You’ll need R andPeakScanner (version 1.0).

After fragment analysis in PeakScanner, copy the generated data table for all samples into a text file (more detailed instructions in main code comments). The code steps through each sample in this file individually, identifying the best matches to known ospC genotypes based on the data peaks.

R code and associated files:

You can figure out how to format your data according to the manuscript and sample file, or you can use these templates. It’s probably about the same amount of effort either way.

PeakScanner setting files (put these in the specified folders within the PeakScanner program folder, and select them within PeakScanner to analyze samples):

This material is based upon work supported by the National Science Foundation under Grant No. 1110472. Any opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation (NSF).