ralowe / windowcount

Count reads from BAM in windows across the genome of interest

windowcount

Count reads from several BAMs in windows across the genome of interest.

Install

Requires pysam (https://pysam.readthedocs.io/en/latest/)

This can be installed using pip

pip install pysam

Then clone repository

git clone https://github.com/ralowe/windowcount.git

Running

windowcount requires 2 inputs. A chromosome sizes file and a directory location of bam files.

To create the chromosome sizes file run samtools (http://www.htslib.org) on .fa file:

samtools faidx ref.fasta

Then run windowcount

python3 main.py -g ref.fasta.fai -d directory/of/BAMS

Full usage can be found by running

python3 main.py

Usage: windowcount -g <chromosome sizes> -d <directory of BAMs>
Options:
	-g		Set the genome chromosome sizes
	-d		Directory to search for BAM files
	-w		Size of window [Int: Default 100]
	-s		Amount of shift between each window [Int: Default 50]
	-o    Output filename [String: Default counts.txt]