VDJ Puzzle [1] is a method to build T-Cell Receptor and B-Cell Receptor assembly from single cell RNA sequencing data.

• TopHat2 for alignament;
• Trinity 2.0.6 for denovo assembly of TCR;
• Ensembl GRCh37 as refernce genome, but it can be easily adapted to other reference genomes (here it is explained how);
• MiGMAP v0.9.7 to build a detailed information table (incoroporates IgBlast);
• Java 1.7 is required by Trinity 2.0.6;

./run_tcr.sh directory_name [options]

grep "TRAC" genes.gtf > TRAC.csv
grep "TRAV" genes.gtf > TRAV.csv
grep "TRAJ" genes.gtf > TRAJ.csv
cat TRAC.csv TRAV.csv TRAJ.csv > TRA.csv

edit TRA.csv in order to have a table with chromosome{tab}starting position{tab}ending position for each TRA gene and rename the file as "TRA.bed". Repeat for TRB adding the command

grep "TRBD" genes.gtf > TRBD.csv

Finally, you need to update the position of the new BED files in run_sc.sh

TCRA=/path_to_bed_files/TRA.bed
TCRB=/path_to_bed_files/TRB.bed