wellDR-seq

This repository contains scripts and meta data metrics files used in the wellDR-seq paper (Coalescing single cell genomes and transcriptomes to decode breast cancer progression). wellDR-seq is a high-throughput single cell sequencing technology that enables simultaneous profiling the whole geneome and transcrptome from thousands of single cells.

Project Overview

This project provides a complete analysis pipeline including data preprocessing, quality control, copy number analysis, gene expression analysis, and multi-omics integration analysis for wellDR-seq data.

Directory Structure

scripts/

R scripts directory contains codes that can reproduce the analysis and figures from the wellDR-seq paper:

• 0_wdr_functions.R: Core function library containing main functions for wellDR-seq analysis
• DNA_QC.R: DNA data quality control and analysis script
• RNA_QC.R: RNA data quality control and analysis script
• gene_dosage.R: Gene dosage analysis script
• sporadic_CNA.R: Sporadic copy number aberrations analysis
• resolution_corr_downsampling.R: Resolution correlation and downsampling analysis
• mutation_calling.sh: Mutation calling shell script
• P1-P12_*_process.R: Processing scripts for 12 different samples
• wdr_mda231_process.R: MDA231 cell line wellDR-seq data processing
• rna_fq_preprocess/: RNA sequencing data preprocessing scripts
  • scDR-fq-convert-v4.pl: Sequencing data format conversion script
  • star-smart.sh: STAR alignment and SMART-seq processing script
  • com_index_wafer.txt: Chip index file

pre_load_data/

Data files required for R script execution:

• pre_load_data.rda: Pre-loaded R data objects
• bin_coords.csv: Genomic bin coordinate information
• hg19_gene_binpos_map.tsv: hg19 genome gene position mapping
• chr_*.txt: Chromosome-related information files
• allcell_markers.csv: Cell marker gene information
• HBCA_Epi_markers.csv: HBCA epithelial cell marker genes
• wafer_match_list.csv: Chip matching list
• bin.boundaries.50k.bowtie.k50.sorted.bin_not_removed.txt: 50kb bin boundary file
• 50kb_excluded.txt: Excluded regions for 50kb bin resolution

Data Source

The original sequencing data from this study has been deposited to the NCBI SRA: PRJNA1086561 and the NCBI GEO: GSE261713.

Citation

If you use the wellDR-seq method in your research, please cite the relevant paper.

Contact

For any additional information, please email the corresponding authors.