TCR/BCR Analysis Pipeline
Pipeline Overview
FASTQ → MiXCR align → Assemble → Export → VDJtools diversity → Visualization
Step 1: MiXCR Processing
# Align reads to V(D)J segments
mixcr align -s hsa -p rna-seq \
R1.fastq.gz R2.fastq.gz \
aligned.vdjca
# Assemble clonotypes
mixcr assemble aligned.vdjca clones.clns
# Export
mixcr exportClones clones.clns clones.txt
Step 2: VDJtools Analysis
# Convert to VDJtools format
vdjtools Convert -S mixcr clones.txt vdjtools/
# Diversity metrics
vdjtools CalcDiversityStats vdjtools/clones.txt diversity/
# Sample overlap
vdjtools CalcPairwiseDistances vdjtools/*.txt overlap/
Step 3: Visualization
# Spectratype plot
vdjtools PlotFancySpectratype vdjtools/clones.txt spectra/
# V usage
vdjtools PlotFancyVJUsage vdjtools/clones.txt usage/
QC Checkpoints
- After alignment: Check V/J assignment rate (>70% typical)
- After assembly: Verify clonotype count and coverage
- After diversity: Compare metrics to expected range
Related Skills
- tcr-bcr-analysis/mixcr-analysis - Detailed MiXCR usage
- tcr-bcr-analysis/vdjtools-analysis - Diversity metrics
- tcr-bcr-analysis/repertoire-visualization - Plots
