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