bap

Bead-based scATAC-seq data Processing

About

This is an integrated python (>= 3.6) and R package that performs analysis and identification of bead doublets and processes data files for downstream analyses for SureCell single-cell ATAC-seq data.

Quality control statistics

Descriptions about QC metrics

Docker

Notes for CAL:

docker build -t caleblareau/bap bap

docker exec -it caleblareau/bap bash

Install

Recommended: First, create a python virtual environment in some working directory to keep things tidy:

python3 -m venv venv3
source venv3/bin/activate

Next, install bap:

git clone https://github.com/caleblareau/bap.git
cd bap
pip3 install -e . 

Verify install:

bap --help

Simple Test

Try a sample analysis on the test .bam file:

cd tests
bap bam -i data/test.small.bam -bt CB

Verify that there are files bap_out/final

Contact

Lead: Caleb Lareau