Outputs

Author: SeekGene

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Updated: 2026-10-13

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scMethyl + RNA-seq Outputs

Output Directory Structure

The final result layout under --outdir is organized as follows:

• fastp/: QC reports for raw FASTQ files and post-barcode-extraction FASTQ files (html/json)
• ${sample}/${sample}_exp/: transcriptome analysis results, including filtered matrices, clustering, and differential expression outputs
• ${sample}/${sample}_methy/step1/: barcode-parsed and sharded methylation FASTQ files
• ${sample}/${sample}_methy/step2/: Bismark BAM files and mapping reports
• ${sample}/${sample}_methy/step3/:
  • split_bams/ and split_bams/merged/: per-cell BAMs, merged BAMs, and barcode counts
  • allcools/ and allcools_generate_datasets/: per-cell ALLC files and MCDS datasets
  • ${sample}_merge_allc.gz and *.CGN-Merge*: merged ALLC outputs
• ${sample}/${sample}_methy/step4/: methylation reduction, clustering, and visualization outputs (*.h5ad, *.pdf, *.png)
• ${sample}/: sample-level summary reports, including methylation summaries and the joint RNA-methylation HTML report
• Nextflow run artifacts (as configured by -c nf/nextflow.config): execution_report.html, execution_timeline.html, pipeline_dag.html, and execution_trace.txt

Important Result Files

Common files and directories include:

• ${sample}_methy_summary.json: summary metrics for methylation processing
• ${sample}_wgs_summary.csv: methylation summary table
• ${sample}_rna_methyl_report.html: integrated transcriptome plus methylation report
• split_bams/: single-cell BAM files grouped by cell barcode
• allcools/: per-cell ALLC files
• allcools_generate_datasets/: MCDS datasets for downstream methylation analysis
• ${sample}.mcds: multi-scale methylation dataset produced by ALLCools
• *.CGN-Merge*: CG context merged ALLC outputs

How to Use Intermediate BAM Outputs

If you need single-cell BAM files for downstream analyses such as CNV or custom post-processing, see:

• How to obtain single-cell BAM files
• How to obtain single-cell BAM files (Chinese)

If you need PCR deduplication for downstream read-count-sensitive analysis, see:

• How to deduplicate single-cell BAM files
• How to deduplicate single-cell BAM files (Chinese)

Notes

• split_bams/ contains raw single-cell alignments and is not PCR-deduplicated by default.
• allcools/ and allcools_generate_datasets/ are the main entry points for methylation downstream analysis.
• The exact presence of some result files depends on the workflow used, especially whether you ran rna_met or methy_only.
• For the methy_only workflow, cell barcode filtering is based on the cell number estimated by the --expected_cell_num parameter (default: 3000).