deepC

A Tensorflow DL framework for predicting Hi-C chromatin interactions using megabase scale DNA sequence.

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Description

This repository contains the core deepC python code, R scripts and functions for downstream analysis as well as tutorials and links to example data.

The core code is implemented in python (v3.5+) and tensorflow (v1). For downstream analysis and visualizations we use R and custom functions for handling HiC data and deepC predictions.

Requirements

• python 3.5 +

• tensorflow (tensorflow-gpu)

  • GPU support is preferable for predictions and essential for training

• additional python modules:

  • numpy (v1.16.4 or above)
  • pysam (tested with v0.15.2)
  • pybedtools and a compatible version of bedtools installed

• R version 3.4.4 +

  • packages:
    • tidyverse (v1.2.1 or above)
    • RColorBrewer (v1.1-2 or above)
    • cowplot (v0.9.2 or above)
    • for plotting 1D tracks (e.g. DNase, ChIP-seq) rtracklayer rtracklayer (v1.38.3 or above) and dependencies are required
  • Rstudio (not required but recommended)

• some processing helper scripts require perl (v5.26.0 or above)

Installation

• Make sure python 3.5-3.7 as supported by tensorflow is installed.

• Install tensorflow preferably with GPU support.

  • We recommend tensorflow 2.1 but deepC was developed under v1.8 and supports (v1.8, 1.14 and 2.1 other versions have not been tested).
  • The tensorflow docker containers are the easiest way to set up tensorflow with GPU and come with the correct CUDA and cuDNN versions packaged.
  • If installing CUDA, cuDNN and tensorflow separately make sure to follow the compatibility advice
  • To install an older version e.g. tensorflow 1 follow this route

• Install additional python library (pysam and pybedtools) using e.g. pip or bioconda

  • pip install pybedtools
  • pip install pysam

• Clone the deepC github repository

• Check which version of tensorflow you have installed and choose the appropriate compatibility version of deepC

tensorflow version	CUDA version	deepC version
2.1+	10.1	tensorflow2.1plus_compatibility_version
2.0	10	tensorflow2.0_compatibility_version*
1.14	10	tensorflow1_version
1.8	9	legacy_version_tf1.8

*Compatibility with v2.0 not yet tested.

Required Resources

• Training deepC models requires running with GPU support for several hours (up to days depending on the dataset and epochs aimed for)
• Running predictions is feasible without but runs significantly faster with a GPU
• For example predicting the impact of a variant as in the tutorial provided requires ~ 5 mins with GPU support and ~ 2h on CPU.

Installation

Clone the repository. Make sure all dependencies are available. To use from within a python script import as import deepCregr.

Tutorials

Find tutorials here.

Trained Models

Download links to trained models are provided under ./models. See the README file there for details.

Publication

Please refer to the Nature Methods article here

Acknowledgements

Implementation of dilated convolutions was adapted from wavenet.