Outputs

Author: SeekGene

Time: 1 min

Words: 129 words

Updated: 2026-02-26

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scMethyl + RNA-seq Outputs

Outputs (by outdir structure)

• fastp/: QC reports for raw and post-barcode FASTQs (html/json)
• ${sample}/${sample}_exp/: Transcriptome analysis directory with filtered matrix, clustering, DE results
• ${sample}/${sample}_methy/step1/: Barcode-parsed and sharded FASTQs
• ${sample}/${sample}_methy/step2/: Bismark BAMs and reports
• ${sample}/${sample}_methy/step3/:
  • split_bams/ and split_bams/merged/: Per-cell BAMs, merged BAMs, barcode counts
  • allcools/ and allcools_generate_datasets/: Per-cell ALLCs and ${sample}.mcds
  • ${sample}_merge_allc.gz, *.CGN-Merge*
• ${sample}/${sample}_methy/step4/: Clustering plots and *.h5ad
• ${sample}/:
  • ${sample}_methy_summary.json, ${sample}_wgs_summary.csv
  • ${sample}_rna_methyl_report.html (if running the main workflow)
• Nextflow run artifacts (as configured by -c nf/nextflow.config): execution_report.html, execution_timeline.html, pipeline_dag.html, execution_trace.txt (script/SeekSoulMethyl/nf/nextflow.config:17)