bio-chipseq-visualization

deepTools - Compute Matrix

Goal: Build a signal matrix of ChIP-seq coverage around reference points for downstream heatmaps and profiles.

Approach: Use computeMatrix to extract bigWig signal values in windows around genomic features like TSS.

## deepTools - Scale-Regions

**Goal:** Visualize ChIP signal across gene bodies scaled to a uniform length.

**Approach:** Scale all gene regions to equal size and compute signal with flanking windows.

```bash

## Signal across gene bodies

computeMatrix scale-regions \
    -R genes.bed \
    -S sample1.bw sample2.bw \
    -b 3000 -a 3000 \              # Flanking regions
    -m 5000 \                       # Scaled body length
    -o matrix_scaled.gz