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+---
+title: "Core Workflows and Tool Categories"
+task: ""
+lineage_type: import
+upstream_source: https://github.com/K-Dense-AI/scientific-agent-skills/blob/991bd993/skills/deeptools/references/core_workflows.md
+upstream_sha: 991bd993
+imported_at: 2026-08-08
+prompt_class: unknown
+upstream_changes: accepted
+author: upstream
+validated: false
+---
+
+# Core Workflows and Tool Categories
+
+Complete command sequences for ChIP-seq quality control, full ChIP-seq analysis, RNA-seq
+coverage, and ATAC-seq analysis, then the tool categories: BAM/bigWig processing, quality
+control, and visualization.
+
+## Core Workflows
+
+deepTools workflows typically follow this pattern: **QC → Normalization → Comparison/Visualization**
+
+### ChIP-seq Quality Control Workflow
+
+When users request ChIP-seq QC or quality assessment:
+
+1. **Generate workflow script** using `scripts/workflow_generator.py chipseq_qc`
+2. **Key QC steps**:
+   - Sample correlation (multiBamSummary + plotCorrelation)
+   - PCA analysis (plotPCA)
+   - Coverage assessment (plotCoverage)
+   - Fragment size validation (bamPEFragmentSize)
+   - ChIP enrichment strength (plotFingerprint)
+
+**Interpreting results:**
+- **Correlation**: Replicates should cluster together with high correlation (>0.9)
+- **Fingerprint**: Strong ChIP shows steep rise; flat diagonal indicates poor enrichment
+- **Coverage**: Assess if sequencing depth is adequate for analysis
+
+Full workflow details in `references/workflows.md` → "ChIP-seq Quality Control Workflow"
+
+### ChIP-seq Complete Analysis Workflow
+
+For full ChIP-seq analysis from BAM to visualizations:
+
+1. **Generate coverage tracks** with normalization (bamCoverage)
+2. **Create comparison tracks** (bamCompare for log2 ratio)
+3. **Compute signal matrices** around features (computeMatrix)
+4. **Generate visualizations** (plotHeatmap, plotProfile)
+5. **Enrichment analysis** at peaks (plotEnrichment)
+
+Use `scripts/workflow_generator.py chipseq_analysis` to generate template.
+
+Complete command sequences in `references/workflows.md` → "ChIP-seq Analysis Workflow"
+
+### RNA-seq Coverage Workflow
+
+For strand-specific RNA-seq coverage tracks:
+
+Use bamCoverage with `--filterRNAstrand` to separate forward and reverse strands.
+
+**Important:** NEVER use `--extendReads` for RNA-seq (would extend over splice junctions).
+
+**Strand note:** `--filterRNAstrand` assumes common dUTP/NSR/NNSR reverse-stranded library preparation. For libraries where read 1 follows the RNA strand, forward/reverse output is inverted; use SAM flag filters when library chemistry differs.
+
+Use normalization: CPM for fixed bins, RPKM for gene-level analysis.
+
+Template available: `scripts/workflow_generator.py rnaseq_coverage`
+
+Details in `references/workflows.md` → "RNA-seq Coverage Workflow"
+
+### ATAC-seq Analysis Workflow
+
+ATAC-seq requires Tn5 offset correction:
+
+1. **Shift reads** using alignmentSieve with `--ATACshift`
+2. **Generate coverage** with bamCoverage
+3. **Analyze fragment sizes** (expect nucleosome ladder pattern)
+4. **Visualize at peaks** if available
+
+Template: `scripts/workflow_generator.py atacseq`
+
+Full workflow in `references/workflows.md` → "ATAC-seq Workflow"
+
+## Tool Categories and Common Tasks
+
+### BAM/bigWig Processing
+
+**Convert BAM to normalized coverage:**
+```bash
+bamCoverage --bam input.bam --outFileName output.bw \
+    --normalizeUsing RPGC --effectiveGenomeSize 2913022398 \
+    --binSize 10 --numberOfProcessors 8
+```
+
+**Compare two samples (log2 ratio):**
+```bash
+bamCompare -b1 treatment.bam -b2 control.bam -o ratio.bw \
+    --operation log2 --scaleFactorsMethod readCount
+```
+
+**Key tools:** bamCoverage, bamCompare, multiBamSummary, multiBigwigSummary, correctGCBias, alignmentSieve
+
+Complete reference: `references/tools_reference.md` → "BAM and bigWig File Processing Tools"
+
+### Quality Control
+
+**Check ChIP enrichment:**
+```bash
+plotFingerprint -b input.bam chip.bam -o fingerprint.png \
+    --extendReads 200 --ignoreDuplicates
+```
+
+**Sample correlation:**
+```bash
+multiBamSummary bins --bamfiles *.bam -o counts.npz
+plotCorrelation -in counts.npz --corMethod pearson \
+    --whatToShow heatmap -o correlation.png
+```
+
+**Key tools:** plotFingerprint, plotCoverage, plotCorrelation, plotPCA, bamPEFragmentSize
+
+Complete reference: `references/tools_reference.md` → "Quality Control Tools"
+
+### Visualization
+
+**Create heatmap around TSS:**
+```bash
+# Compute matrix
+computeMatrix reference-point -S signal.bw -R genes.bed \
+    -b 3000 -a 3000 --referencePoint TSS -o matrix.gz
+
+# Generate heatmap
+plotHeatmap -m matrix.gz -o heatmap.png \
+    --colorMap RdBu --kmeans 3
+```
+
+**Create profile plot:**
+```bash
+plotProfile -m matrix.gz -o profile.png \
+    --plotType lines --colors blue red
+```
+
+**Key tools:** computeMatrix, plotHeatmap, plotProfile, plotEnrichment
+
+Complete reference: `references/tools_reference.md` → "Visualization Tools"