readme update

README.md

@@ -1 +1,19 @@
-# Chromatin-GNN: Graph representation learning for 3D genome architecture
+# Graph learning for genome architecture
+
+### workflow
+
+```bash
+# Build graph (contact matrix & bigwig needed)
+python scripts/build_graph.py --mcool x.mcool --chrom chrx --res x
+  --bigwigs xCTCFx.bw xH3K27me3x.bw --out data/chrx_xconditionx.pt
+
+# Train model
+python scripts/train_vgae.py --graph data/chrx_xconditionx.pt --epochs 100 --outdir results
+
+# Encode treatment graph
+python scripts/encode_graph.py --model results/model.pt --graph data/chrx_xtreatmentx.pt --out results/emb_xtreatmentx.npy
+
+# Compare embeddings
+python scripts/compare_embeddings_general.py --emb1 results/emb.npy --emb2 results/emb_xtreatmentx.npy \
+  --label1 xControlx --label2 xTreatmentx --prefix results/chrx
+```