This workflow summarises the different commands to run. Step-by-step examples using test data or the GSE35626 public dataset are also available for a more detailed explanation. See also the preprint of our application note deposited in bioRxiv.
Data preparation in the command line
Convert sequencer ouptut files from Sanger or 454 sequencers. Single-end Illumina sequence output can be used directly. Paired-end sequences need to be merged.
ClonotypeR is ran in two steps.
clonotypeR detectcompares the sequences to a reference database of V segments.
clonotypeR extractsearches for J segments in sequences where a V segment was found, extracts the CDR3s and reports the results in a table ready to be loaded in R.
See the manual page of
clonotypeR for more details.
Data analysis in R
The R package can be loaded with the following command.
The file produced by
clonotypeR extract is loaded by the
read clonotypes(). Expression tables are calculated by the
clonotype table(). These tables are the basis for the analysis, to compare clonotype profiles, cluster the samples, calculate overlaps, etc.
See the list of functions for more information.