Outputs¶

Quality control¶

Omnomnomics writes per-sample BAM statistics and PDF/SVG summaries, an experiment-level QC table and figures, and a MultiQC report unless disabled. Flow summaries combine raw/trimmed read counts, mapper alignment statistics, and post-filter BAM metrics. Cached lightweight metrics allow reporting after safe intermediate cleanup.

RNA¶

• DE_calling/*.raw_read_quant.table.txt: featureCounts matrix
• DE_calling/<analysis>/: differential tables, plots, enrichment, and scripts
• BigWigs/*.plus.bw and *.minus.bw: stranded signal
• merged_hubs/*.hub/: grouped UCSC track hubs

ATAC and ChIP¶

• peak_calling/: peaks or assay-specific feature definitions
• peak_calling/analyze_peaks/: unions, intersections, annotations, and signal summaries
• DE_calling/: count matrix and differential chromatin results
• DE_calling/analyze_peaks_de/: significant sets, signal plots, motifs, and status tables

Important post-DE audit tables include:

• summary/set_manifest.tsv
• summary/analyze_peaks_de_report.tsv
• signal/signal_runs.tsv
• motifs/motif_runs.tsv

Statuses explicitly distinguish new results, reused results, intentional skips, timeouts, failures, and valid no-enrichment outcomes.