BCR Clonotype Analysis from Single-Cell RNA-seq

This project analyzes B cell receptor (BCR) sequences from single-cell RNA-seq data using the V(D)J output generated by the Cell Ranger pipeline. The goal is to assess immunoglobulin chain usage and clonotype frequency.

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📘 Project Overview

This analysis extracts and summarizes BCR clonotype information from 10x Genomics single-cell V(D)J sequencing data. The input includes:

• all_contig_annotations.csv to identify and separate immunoglobulin heavy (IGH), kappa (IGK), and lambda (IGL) chains
• clonotypes.csv to quantify and visualize clonotype frequency and chain usage

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📊 Analysis Tasks

Task 1: Parsing and Saving Immunoglobulin Chain Data

• Read all_contig_annotations.csv from Cell Ranger VDJ output
• Filter and extract entries for:
  • IGH (immunoglobulin heavy chain)
  • IGK (kappa light chain)
  • IGL (lambda light chain)
• Save each chain as a separate CSV for downstream analysis

Task 2: Clonotype Frequency and Chain Usage Visualization

• Read clonotypes.csv and count occurrences of each clonotype
• Visualize clonotype frequencies using bar plots
• Calculate the proportion of IGK, IGL, and IGH chain usage across clonotypes
• Create pie plots to illustrate the distribution of immunoglobulin light and heavy chains

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💡 Notes

• Raw data is not publicly available due to client ownership and confidentiality.
• Some example outputs plots are organized by task in the output/ folder.
• This project is designed for both reproducibility and clarity.

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📬 Contact

Author: Nasim Rahmatpour Email: nasimrahmatpour1@gmail.com GitHub: (https://github.com/nasimbio)