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Quality Control

HOMERun writes detailed per-sample QC under Species/QC/<sample>/ and cross-condition plots directly under Species/QC/.

Per-sample output

Available inputs determine which plots are produced. Outputs can include:

  • trimming and alignment summaries;
  • read-length, nucleotide-frequency, and autocorrelation plots;
  • combined and per-replicate tag-directory statistics;
  • TSR summary and annotation plots;
  • promoter-proximal versus distal TSS counts;
  • RIT/RIE metrics when a GTF is configured.

Missing optional inputs cause the relevant plot to be skipped with a log message; they do not invalidate unrelated QC.

Cross-condition nucleotide divergence

For each species, assay, and nucleotide, HOMERun compares condition-preserving combo TagDirs against the global mean. It writes:

Species/QC/csRNA_A_DivergentPlot.png
Species/QC/csRNA_A_DivergentPlot.svg
Species/QC/csRNA_A_Divergent_Data.tsv

Equivalent C, G, and T files are produced, along with sRNA files when sRNA combos exist. Rows retain the sample and full condition-combo label, and day labels such as D2 and D10 are sorted naturally.

Workbook

The QC step also writes a species-level Excel workbook containing the underlying summary tables, including detailed TSR statistics. Use the workbook for filtering and downstream review; use the PNG/SVG files for quick visual inspection and reports.