Plot read depth per transcript

Requirements

• python3
  
• wkhtmltopdf
  
• python package: Pillow, gffutils, pybedtools, binaryornot, yaspin (0.12.0), tqdm

Installation

wget https://github.com/wkhtmltopdf/wkhtmltopdf/releases/download/0.12.4/wkhtmltox-0.12.4_linux-generic-amd64.tar.xz
tar -xvf wkhtmltox-0.12.4_linux-generic-amd64.tar.xz
cd wkhtmltox
sudo cp -R ./* /usr/
git clone https://github.com/dooguypapua/CovPlotter.git
cd CovPlotter
pip3 install -r requirements.txt

Usage

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  /   _   |__)| _ |_|_ _ _ 
  \__(_)\/|   |(_)|_|_(-|  
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  USAGE: CovPlotter.py [OPTIONS] -g genes.txt -i listBam.txt -o output
         CovPlotter.py [OPTIONS] -n ACAD,OPA1 -i listBam.txt -o output
         CovPlotter.py [OPTIONS] -l genes.bed -i listBam.txt -o output

  [OPTIONS]
      -ref       STR      Reference hg19/hg20      (default: hg19)
      -db        STR      Database refseq/ensembl  (default: refseq)
      -tmp       DIR      Temporary folder         (default: /tmp)
      -nt        INT      Threads number           (default: 1)
      -color     BOOL     Terminal color           (true or false)
      -h,--help
      -v,--version