ChromBPNet training

Lets get started with training a ChromBPNet model with a pre-trained bias model on the downloaded and preprocessed tutorial data.

Step 1

We will first start by downloading a pre-trained bias model provided with this repo here.

mkdir ~/bias_model
wget https://mitra.stanford.edu/kundaje/oak/akundaje/anusri/chrombpnet_data/input_files/bias_models/ATAC/ENCSR868FGK_bias_fold_0.h5 -O ~/bias_model/ENCSR868FGK_bias_fold_0.h5

• TODO: Add Notes on how to pick a bias model

Step 2

Use the pre-trained bias model to train a bias-factorized ChromBPNet model

train_chrombpnet_model.sh \
  -i /path/to/input.bam \
  -t "bam" \
  -d "ATAC" \
  -g /path/to/hg38.fa \
  -c /path/to/hg38.chrom.sizes \ 
  -p /path/to/peaks.bed \
  -n /path/to/nonpeaks.bed \
  -f /path/to/fold_0.json \
  -b /path/to/bias.h5 \ 
  -o path/to/output/dir/ \