Although a number of sequencers are currently available for deep sequencing, most researchers use Illumina next-generation platforms due to the high number of molecules (tag count) that can be sequenced per sample. Tag count represents the most instrumental parameter of output sequencing quality. The number of tags that need to be sequenced depends on the goal of the specific experiment, with nucleosome mapping and TF footprinting experiments requiring higher coverage compared to standard chromatin accessibility detection. To obtain a target coverage depth per sample, the researcher should take into account the minimal number of mappable tags delivered by the instrument in use and adjust accordingly the number of multiplexed samples per lane of flow cell (for details read [31]). A secondary parameter of sequencing quality is tag length, which is mainly a function of the applied sequencing chemistry and currently varies between approximately 36 to 300 bp. Generally speaking, paired-end and longer-read sequencing provides the most accurate results and is recommended whenever possible, especially for areas of the genome with low-complexity or many repetitive elements [31, 104]. However, in most experimental cases chromatin accessibility can be accurately determined with single-end, shorter-length reads without the unnecessary additional expense.
