Hello! I'm performing a single-cell genome-wide copy-number profiling by low-pass sequencing (coverage: 1X, 0.5X, 0.1X). Would anybody suggest me how to determine which is the optimal bin size in the genome segmentation step? Usually it's set to 0.5M or 1M when the genome coverage is as low as 1X. I would like to know which is the best one for my coverage, any advice? Thank you!
The first author of this paper has developed an interactive app that lets you play around with your sample characteristics and see how that would affect the required read depth to be able to perform CNV calling: https://gmacintyre.shinyapps.io/sWGS_power/