PeakATail

Base installation

• you should have samtools and bedtools installed

  on your system

  sudo apt-get install bedtools

  sudo apt-get install samtools

install

• clone repo

  git clone https://github.com/BMGLab/PeakATail.git

• go to project directory

  cd PeakATail

• open python env

  python3.10 -m venv .venv

Venv

• activate environment

  source ,venv/bin/activate

• install requierments

  pip install -r requirments.txt

• install ema
• use -e flag to could able automatic updates

  pip install -e .

Run

• ema merge

• use to merge multiple bam files

  ema_merge --bamFiles bamfiles.yaml --threads 4

• Example yaml File

• ema

• this command peakcall and cluster base on PAS

  ema --bamDir path/to/merged.bam \
      --sequenceLen 98 \
      --CellBarcodeLen 16 \
      --BarcodeTag CB \
      --gtfDir path/to/human.gtf
  

• or you could have all in a single line