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