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TCR sequencing

  • This is the workflow of TCR sequencing and analysis for tumor TCR repertoire contraction / oligoclonality study
  • Raw sequencing datas were processed through MiXCR for clonotype observation and analyzed with Immunarch as well as VDJviz

Pipeline workflow

Which includes:

  1. QC test: FastQC + MultiQC
  2. Alignment: MiXCR
  3. Assemble Clones: MiXCR
  4. Export txt files: MiXCR
  5. Bulk TCR exploration (R Studio): Immunarch
  6. Circos plot (VDJviz browser): VDJviz

Environments

  • MiXCR v3.0.13
  • Python v3.6.13
  • Snakemake v5.7.0

Input data

  • Paired-end fastq files obtained from 5’RACE TCR sequencing TAKARA SMARTer, total 16 fastq files
  • Create soft link $ln -s path/to/data/
  • Bulk datas were obtained from B6 mice(CTRL/tumor-treated groups)
  • Metadata:
Sample Number Tissue Chain Type Source Batch N
1418-LN-TCR-a 1418 LN TCR-a Ctrl TGIA 1 5
1418-LN-TCR-b 1418 LN TCR-b Ctrl TGIA 1 5
1418-SP-TCR-a 1418 SP TCR-a Ctrl TGIA 1 5
1418-SP-TCR-b 1418 SP TCR-b Ctrl TGIA 1 5
6973-LN-TCR-a 6973 LN TCR-a MTCQ1 TGIA 1 5
6973-LN-TCR-b 6973 LN TCR-b MTCQ1 TGIA 1 5
6973-SP-TCR-a 6973 SP TCR-a MTCQ1 TGIA 1 5
6973-SP-TCR-b 6973 SP TCR-b MTCQ1 TGIA 1 5

Output data

  • txt files

Run Snakefile

Run Snakefile by snakemake -p -j 20

Download sample.txt file from Linux to desktop

Navigate to desktop's local terminal and enter the following command at command line:

$scp LinuxUserName@avisIP:sample.txt_file_path ~/Desktop/

References

MiXCR Documantation

Immunarch Documentation

Load MiXCR files into Immunarch

The new synthesis of diversity indices and similarity measures