How much should I Downsample?
I have a single cell data processed with CITE seq technology. We are hoping to downsample it so that it takes less time to process and can be used to test a pipeline that we are working on. How much should I downsample on the read level?
I have seen people downsample down to 20% using seqtk. I want to preserve some biological significance to the data. What do you guys think would be a safe percentage?
Thanks in advance :)