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PromID: A deep learning-based tool to identify promoters

Project description

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.

Project details


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