You can additionally build a graph of hypermutations for the sample using
java -jar MIGEC.jar CreateCdrHypermGraph final/S1.cdr3blast.txt net
which will generate files that allow fast network construction using Cytoscape’s network from table and import table routines for further data exploration.
Note that translated CDR3 sequences are obtained by simultaneously
translating codons in two directions: from V and J segments to the
middle of CDR3. If a frameshift is detected, the incomplete codon is
added in lower case, with missing nucleotides marked as
codons are marked by
*. CDR3 that contain either frameshift or stop
codon are non-functional and are filtered by default. To include them
into your output use
We also recommend to try out our new VDJtools software suite to perform post analysis of clonotype tables generated by MIGEC.