From bdd3516e9dbd47e593132f33269f2731e6a2f309 Mon Sep 17 00:00:00 2001
From: aman <aman.nalakath@tum.de>
Date: Thu, 23 Oct 2025 09:13:46 +0200
Subject: [PATCH] readme update

---
 README.md | 20 +++++++++++++++++++-
 1 file changed, 19 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 62b1af1..096be89 100644
--- a/README.md
+++ b/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
+```
\ No newline at end of file