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.
Your English is excellent - it's more coherent and better edited than most native speakers on the site.
As for your question, the number of cells isn't as important as DNA quantity/quality at the end of your prep. Ultimately, I wouldn't worry much about this, as ATAC has an excellent signal to noise ratio and pretty much any processing pipeline accounts for biases like sequencing depth. This is particularly true if you're only comparing whether a region is accessible or not (i.e. a binary peak presence/absence study) rather than trying to compare signal across samples (quantitative comparisons, which are a tougher nut to crack).