--- a
+++ b/script/run_scMDC_script.sh
@@ -0,0 +1,19 @@
+#!/bin/bash -l
+#SBATCH --gres=gpu:1
+
+#Here are the commands for the real data experiments. We test ten times on each dataset.
+
+f=../datasets/CITESeq_GSE128639_BMNC_annodata.h5
+echo "Run CITE-seq BMNC"
+python -u run_scMDC.py --n_clusters 27 --ae_weight_file AE_weights_bmnc.pth.tar --data_file $f --save_dir citeseq_bmnc /
+--embedding_file --prediction_file --filter1
+
+f=../datasets/SMAGESeq_10X_pbmc_granulocyte_plus.h5
+echo "Run SMAGE-seq PBMC10K"
+python -u run_scMDC.py --n_clusters 12 --ae_weight_file AE_weights_pbmc10k.pth.tar --data_file $f --save_dir atac_pbmc10k /
+--embedding_file --prediction_file --filter1 --filter2 --f1 2000 --f2 2000 -el 256 128 64 -dl1 64 128 256 -dl2 64 128 256 -phi1 0.005 -phi2 0.005 -signma2 2.5 -tau .1
+
+f=../datasets/CITESeq_realdata_spleen_lymph_111_anno_multiBatch.h5
+echo "Run multi-batch CITE-seq SLN111"
+python -u run_scMDC_batch.py --n_clusters 35 --ae_weight_file AE_weights_sln111.pth.tar --data_file $f --save_dir citeseq_sln111 /
+--embedding_file --prediction_file --filter1