Predict drosophila enhancer activity based on DNA sequence
Dataset can be downloaded from Stark lab, repo for original DeepSTARR CNN solution here
To download data run:
# FASTA files with DNA sequences of genomic regions from train/val/test sets
wget 'https://data.starklab.org/almeida/DeepSTARR/Data/Sequences_Train.fa'
wget 'https://data.starklab.org/almeida/DeepSTARR/Data/Sequences_Val.fa'
wget 'https://data.starklab.org/almeida/DeepSTARR/Data/Sequences_Test.fa'
# Files with developmental and housekeeping activity of genomic regions from train/val/test sets
wget 'https://data.starklab.org/almeida/DeepSTARR/Data/Sequences_activity_Train.txt'
wget 'https://data.starklab.org/almeida/DeepSTARR/Data/Sequences_activity_Val.txt'
wget 'https://data.starklab.org/almeida/DeepSTARR/Data/Sequences_activity_Test.txt'No preporcessing is needed, we use train/valid/test as in the original dataset:
train/valid/test = 402296/40570/41186 samples
Set paths to the data, edit hyperparameters in example script finetune_deepstarr.sh and run training:
CUDA_VISIBLE_DEVICES=0 NP=1 ./finetune_deepstarr.sh