EPCOT: A computational tool to use ATAC-seq to impute epigenome, transcriptome, and high-resolution chromatin contact maps

[ Code / Documentation ] [ Paper ] [ Google Colab Notebook ]

Instructions:

  • Use the first app to process ATAC-seq data by entering a Google Drive or Dropbox link of ATAC-seq BAM file. It is recommaneded to use ENCODE ATAC-seq pipeline to generate the BAM file.
  • Execute the model by uploading the processed ATAC-seq file to the “Run Model” interface in the second app.
  • Visualize the prediction results by uploading the predicted files from the “Run Model” interface to the “Visualize Prediction Results” interface.

We provide detailed instructions for running the apps on Google Colab notebook with free GPUs Open In Colab

App 1: Process ATAC-seq data

Notice:

  • Downsample the BAM file (to around 30M alignments) before upload if the size is too large.
  • The processed file can also be obtained by running python scripts on your own server, if the running time is too long.

    • Open in Hugging Face Space

    App 2: Run models and visualize prediction results

    Open in Hugging Face Space