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.
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