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.

Usage

PromID can be run from the command line:

promid -I hg19.fa -O hg19_promoters.bed

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.
• -T1: Decision threshold for the scan model, defaults to 0.2.
• -T2: Decision threshold for the prediction model, defaults to 0.5.