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

• https://mixcr.readthedocs.io/en/master/quickstart.html

Immunarch Documentation

• https://immunarch.com/

Load MiXCR files into Immunarch

• https://immunarch.com/articles/web_only/load_mixcr.html#loading-a-folder

The new synthesis of diversity indices and similarity measures

• http://www.loujost.com/Statistics%20and%20Physics/Diversity%20and%20Similarity/EffectiveNumberOfSpecies.htm