Data Preparation

Author: SeekGene

Time: 2 min

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Updated: 2026-05-28

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scMethyl + RNA-seq Data Preparation

Download Reference Database

# Download human reference genome (GRCh38)
wget -dc -O human-reference-GRCh38.tar.gz "https://seekgene-public.oss-cn-beijing.aliyuncs.com/methy_demo/methy_exp/v1.1/human-reference-GRCh38.tar.gz"
wget -dc -O human-reference-GRCh38.tar.gz.md5 "https://seekgene-public.oss-cn-beijing.aliyuncs.com/methy_demo/methy_exp/v1.1/human-reference-GRCh38.tar.gz.md5"

# Download mouse reference genome (GRCm39)
wget -dc -O mouse-reference-GRCm39.tar.gz "https://seekgene-public.oss-cn-beijing.aliyuncs.com/methy_demo/methy_exp/v1.1/mouse-reference-GRCm39.tar.gz"
wget -dc -O mouse-reference-GRCm39.tar.gz.md5 "https://seekgene-public.oss-cn-beijing.aliyuncs.com/methy_demo/methy_exp/v1.1/mouse-reference-GRCm39.tar.gz.md5"

# Extract reference genomes
tar -xzf human-reference-GRCh38.tar.gz
tar -xzf mouse-reference-GRCm39.tar.gz

Download Test Data (Optional)

For downloading demo data, please refer to the Datasets document.

Repository Layout

After cloning, the key Nextflow entry points and modules are:

• nf/main.nf: Main workflow for transcriptome + methylation end-to-end processing.
• nf/methy_only.nf: Workflow for methylation-only data.
• nf/modules/: Step-wise process modules:
  • step1.nf preprocessing, QC, barcode extraction, transcriptome analysis.
  • step2.nf Bismark alignment and BAM sorting.
  • step3.nf per-cell BAM splitting, ALLC generation/merge, multi-scale datasets.
  • step4.nf summaries, dimensionality reduction, joint report.
  • utils.nf helpers for methylation-only workflow (reads counting and cell estimation).
• nf/bin/: Helper scripts and resources (e.g., barcode whitelists).
• nf/nextflow.config: Executors and resource configuration.
• sc_methy_workflow.sh: Shell script to run the dual-omics analysis pipeline.

We provide two methods for data analysis:

1. Shell Script: Run the analysis pipeline directly via the sc_methy_workflow.sh script.
2. Nextflow Pipeline: Run the Nextflow pipeline via nf/main.nf.

Details of both methods are provided below.