README.md

chrombpnet

Make scripts

1. Negatives

2. Bias pipeline

3. Run ChromBPNet pipeline

cmd="./SLURM/chrombpnet_pipeline.sh \
-s scripts/chrombpnet_pipeline/HPAP_chrombpnet_pipeline.sh \
-j HPAP_chrombpnet_pipeline \
-p carter-gpu \
-a carter-gpu \
-g a30:1 \
-c 4 \
-m 80G \
-t 14-00:00:00 \
-o /cellar/users/aklie/data/datasets/HPAP/bin/slurm_logs/chrombpnet/chrombpnet_pipeline \
-n 12 \
-x 3"
echo -e "Running command:\n$cmd"
eval $cmd

Making predictions

cmd="./SLURM/predicitons.sh \
-s scripts/predictions/HPAP_predictions.sh \
-j HPAP_predictions \
-p carter-gpu \
-a carter-gpu \
-g 1 \
-c 4 \
-m 80G \
-t 14-00:00:00 \
-o /cellar/users/aklie/data/datasets/HPAP/bin/slurm_logs/chrombpnet/predictions \
-n 12 \
-x 3"
echo -e "Running command:\n$cmd"
eval $cmd