FAIRE-extracted DNA fragments can be analyzed in a high-throughput way using next-generation sequencing techniques. In general, libraries are made by ligating specific adapters to the DNA fragments that allow them to cluster on a platform and be amplified resulting in the DNA sequences being read/determined, and this in parallel for millions of the DNA fragments.
Depending on the size of the genome  FAIRE-seq is performed on, a minimum of reads is required to create an appropriate coverage of the data, ensuring a proper signal can be determined. In addition, a reference or input genome, which has not been cross-linked, is often sequenced alongside to determine the level of background noise.
Note that the extracted FAIRE-fragments can be quantified in an alternative method by using quantitative PCR. However, this method does not allow a genome wide / high-throughput quantification of the extracted fragments.