I'm a student learning bioinformatics from scratch, and our lab is planning to perform ATAC-seq on rare population cells in HSCs ( around 5k-20K ) for the first time ever. I need your help. The cells will be sorted before the transposase reaction, but we are having difficulties in getting a comparable or consistent number of cells across the conditions because the counting method is not reliable with a small number of cells. ( 4 biological replicates on control and sample, no technical replicates ) My boss is skeptical about making libraries out of samples with different cell numbers. I'm wondering if this is serious issues and if we can address the negative consequence of this later through processing. I'm sorry if the question was difficult to understand due to poor English.