I want to split the PBMC scATAC bam from 10x by cluster id. So, I can then make a bigwig for each cluster to visualize in IGV.
The first thing I did was googling to see if anyone has written such a tool (Do not reinvent the wheels!). People have done that because I saw figures from the scATAC papers. I just could not find it. Maybe I need to refine my googling skills.
I decided to write one myself. The following is my journey for this small task.
download the 5k pbmc scATAC data from <a href=“https://support.10xgenomics.com/single-cell-atac/datasets/1.0.1/ …