PromID: A deep learning-based tool to identify promoters

Installation

PromID can be installed from the github repository:

git clone https://github.com/PromStudy/PromID.git
cd PromID
pip install .

PromID requires tensorflow>=1.7.0, the GPU version is highly recommended. First, install Conda and create the environment:

conda create -n PromID python=3.6
conda activate PromID

Next, install tensorflow:

conda install -c conda-forge tensorflow==1.7.0

OR

conda install -c conda-forge tensorflow-gpu==1.7.0

for the GPU version. If that does not work, try removing "-c conda-forge".
If you chose the GPU version, please also install CUDA9 and cuDNN7:

conda install cudatoolkit=9.0
conda install cudnn=7.1.2=cuda9.0_0

Usage

PromID can be run from the command line:

promid -I hg19.fa -O hg19_promoters.bed -C chr20

Required parameters:

• -I: Input fasta file.
• -O: Output bed file.

Optional parameters:

• -D: Minimum soft distance between the predicted TSS, defaults to 1000.
• -C: Comma separated list of chromosomes to use for promoter prediction, defaults to all.
• -T: Decision threshold for the prediction model, defaults to 0.5.