We use qPCR based methods to quantify our ATAC-seq libraries. We have found that other methods, such as Qubit, can potentially give misleading and inaccurate results due to variation within the fragment size distribution. We recommend quantifying libraries using the KAPA Library Quant Kit for Illumina Sequencing Platforms (KAPABiosystems). Alternately, integrated Bioanalyzer traces can be used to approximate library concentration.
