VDJ Puzzle [1] is a method to build T-Cell Receptor and B-Cell Receptor assembly from single cell RNA sequencing data.
VDJ Puzzle requires the following tools:- 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
from VDJPuzzle directory ```bash ./VDJPuzzle.sh Example ``` You can post any question or issue to our Google group
or by email ( s.rizzetto at student.unsw.edu.au ) [1] Auda Eltahla\*, Simone Rizzetto\*, Mehdi Rasoli\*, Brigid Betz-Stablein, Vanessa Venturi, Katherine Kedzierska, Andrew R Lloyd, Rowena A Bull and Fabio Luciani. Linking the T cell receptor to the single cell transcriptome in antigen-specific human T cells. Immunology and cell biology, 2016, doi: 10.1038/icb.2016.16G