Introduction

This software is used for calculating copy number of genes, and get top 5% genes which selected by humans.

popCNV CLI version

Dependencies

Python modules:

• numpy
• scipy
• pysam
• pathos

Software:

• mosdepth

Installation

cd /path/to/install
git clone https://github.com/sc-zhang/popCNV.git
cd popCNV.py
chmod +x popCNV.py
echo 'export PATH=/path/to/install/popCNV.py:$PATH' >> ~/.bash_profile
source ~/.bash_profile

Usage

Notice: you need add mosdepth to your PATH

usage: popCNV.py [-h] -g GENOME -b BAM [-s WIN_SIZE] -l LIST -w WORKDIR --group GROUP --wild WILD [-t THREADS]

options:
  -h, --help            show this help message and exit
  -g GENOME, --genome GENOME
                        Input genome fasta file
  -b BAM, --bam BAM     Directory of bam files
  -s WIN_SIZE, --win_size WIN_SIZE
                        window size, default=1000
  -l LIST, --list LIST  List file contain 4 columns: chromosome_name start_position end_position gene_name
  -w WORKDIR, --workdir WORKDIR
                        Working directory
  --group GROUP         Group file contain 2 columns: sample_name group_name(without space)
  --wild WILD           Wild group id
  -t THREADS, --threads THREADS
                        Threads

Results

File/Directory	Description
06.genes.round.cn	Copy number of genes in all groups
07.RFD	RFD is relative frequency difference which was calculated based on wild group a) a set of list files named with group_name, contain a list of genes with top 5% of RFD based on p<0.05 b) total.list contains all RFD and p-value of genes in all groups

popCNV GUI version

Installation

Download executable file in releases.

Usage

Notice: you need run mosdepth with same window size for all your samples, and get sequence depth of all samples manually.

# For windows user, just run gpopCNV.exe, for other platform like linux and macOS,
# use command below to run gpopCNV
python3 gpopCNV.py

The main form is like below: