Initial commit

skills/deeptools/assets/quick_reference.md

@@ -0,0 +1,58 @@
+# deepTools Quick Reference
+
+## Most Common Commands
+
+### BAM to bigWig (normalized)
+```bash
+bamCoverage --bam input.bam --outFileName output.bw \
+    --normalizeUsing RPGC --effectiveGenomeSize 2913022398 \
+    --binSize 10 --numberOfProcessors 8
+```
+
+### Compare two BAM files
+```bash
+bamCompare -b1 treatment.bam -b2 control.bam -o ratio.bw \
+    --operation log2 --scaleFactorsMethod readCount
+```
+
+### Correlation heatmap
+```bash
+multiBamSummary bins --bamfiles *.bam -o counts.npz
+plotCorrelation -in counts.npz --corMethod pearson \
+    --whatToShow heatmap -o correlation.png
+```
+
+### Heatmap around TSS
+```bash
+computeMatrix reference-point -S signal.bw -R genes.bed \
+    -b 3000 -a 3000 --referencePoint TSS -o matrix.gz
+
+plotHeatmap -m matrix.gz -o heatmap.png
+```
+
+### ChIP enrichment check
+```bash
+plotFingerprint -b input.bam chip.bam -o fingerprint.png \
+    --extendReads 200 --ignoreDuplicates
+```
+
+## Effective Genome Sizes
+
+| Organism | Assembly | Size |
+|----------|----------|------|
+| Human | hg38 | 2913022398 |
+| Mouse | mm10 | 2652783500 |
+| Fly | dm6 | 142573017 |
+
+## Common Normalization Methods
+
+- **RPGC**: 1× genome coverage (requires --effectiveGenomeSize)
+- **CPM**: Counts per million (for fixed bins)
+- **RPKM**: Reads per kb per million (for genes)
+
+## Typical Workflow
+
+1. **QC**: plotFingerprint, plotCorrelation
+2. **Coverage**: bamCoverage with normalization
+3. **Comparison**: bamCompare for treatment vs control
+4. **Visualization**: computeMatrix → plotHeatmap/plotProfile