I am manipulating some BAM files using
pysam package which seems to be very fast and handy. However, I ran into problem when I am trying to generate bigWig files from BAM files in Python. I used
deeptools to do this previously, but it is a standalone tool that cannot be used from within my Python scripts.
Therefore, I am wondering what Python package would allow me to read in BAM files and convert them to bigWig files.