My lab is going to work on ATAC for the first time and I have been asked as to what is amount of sequencing we need to do. We want to end up with 50million aligned reads. So my question is what is the ballpark mapping rate that is observed for ATAC data. We are planning on doing 100bp paired-end reads.
My search led to this post where it seems the mapping rate can vary between 50% to 90% (https://www.biostars.org/p/170294/). Any further light on what is generally seen would be helpful.