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Outputs

All SeqNado analysis results are organized within the seqnado_output/ directory (or your custom output directory). This page describes the general structure and types of files you can expect.

General Structure

The output directory follows a structured organization:

  • qc/: Quality control reports (FastQC, MultiQC, etc.)
  • alignments/: BAM files and indexing information.
  • peaks/: (Assay-specific) Peak calling results (BED, BEDGraph, peaks files).
  • tracks/: BigWig tracks for visualization in genome browsers.
  • plots/: Diagnostic plots, heatmaps, and TSS enrichment plots.
  • report/: Summary reports of the entire pipeline run.
  • geo/: (Optional) Prepared metadata and symlinks for GEO submission.

Assay-Specific Outputs

ATAC-seq and ChIP-seq

  • Peaks: Found in peaks/ using MACS2 or other specified callers.
  • Coverage: BigWig tracks generated in tracks/, often scaled or normalized.
  • QC: TSS enrichment scores and fragment size distributions in qc/.

RNA-seq

  • Quantification: Gene and transcript level counts in quant/.
  • Alignments: Genomic coordinates BAM files in alignments/.

CUT&Tag (CAT)

  • Peaks: Peaks in peaks/ with SEACR or configured caller.
  • Coverage: BigWigs in tracks/ optimized for small fragments.
  • QC: Low-input focused metrics (e.g., fragment size summaries) in qc/.

SNP Analysis (SNP)

  • Variants: VCF/BCF files and summaries in variants/ (if enabled).
  • Alignments: Sorted/indexed BAMs in alignments/.
  • QC: Mapping/variant-calling metrics in qc/.

Methylation (METH)

  • Methylation Calls: Cytosine/CpG reports (e.g., BED/bedGraph) in methylation/.
  • Alignments: BAMs in alignments/ (bisulfite-aware processing).
  • QC: Conversion rates and summary metrics in qc/.

MCC (MCC)

  • Contacts: Contact maps/matrices (e.g., cooler or equivalent formats) in interactions/.
  • Peaks/Enrichment: MCC-specific enrichment or peak outputs in peaks/ (if configured).
  • QC: MCC run metrics and summaries in qc/.

CRISPR Screens (CRISPR)

  • Guide Counts: Count tables per guide/target in quant/ or counts/.
  • Screen Analysis: Differential hit results (e.g., MAGeCK outputs) in report/ or analysis/.
  • QC: Library representation and mapping metrics in qc/.

Multiomics (MULTIOMICS)

  • Per‑Assay Outputs: All of the above, organized under a common project with per‑assay subfolders.
  • Integrated Reports: Cross‑assay summaries in report/ and combined plots in plots/.

Summary Report

The primary entry point for exploring your results is the seqnado_report.html found in the report/ folder. It provides an interactive overview of all samples and QC metrics.

To rerun or adjust resources/presets, see the CLI reference: seqnado pipeline.