Outputs
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Updated: 2026-05-12
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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${sample}/${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/: per-cell BAMs, merged BAMs, ALLC files, merged ALLC files, and MCDS datasets${sample}/${sample}_methy/step4/: methylation reduction, clustering, and visualization outputs${sample}/: sample-level summary reports, including methylation summaries and the joint RNA-methylation HTML report- Nextflow run artifacts:
execution_report.html,execution_timeline.html,pipeline_dag.html, andexecution_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${sample}_rna_methyl_report.html: integrated transcriptome plus methylation reportsplit_bams/: single-cell BAM files grouped by cell barcodeallcools/: per-cell ALLC filesallcools_generate_datasets/: MCDS datasets for downstream methylation analysis${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:
If you need PCR deduplication for downstream read-count-sensitive analysis, see:
Notes
split_bams/contains raw single-cell alignments and is not PCR-deduplicated by default.allcools/andallcools_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_metormethy_only.