Table 3:

Guidelines for sequencing parameters

Application	Insight gained	Minimum Read Length†	Index Length*	Paired- or single- end	Read- pairs per sample
Gene regulatory landscape profiling	Peaks, differential peaks between samples, motif analysis of peaks	36 bp	8	Paired	10 million
Genotyping	Gene regulatory landscape + genotype of sample; useful for patient samples and to determine if sequence variants affect a peak.	100 bp	8	Paired	10 million
Footprinting Analysis	Footprinting of different TFs to determine binding sequence at base-pair resolution	36 bp	8	Paired	200 million
Nucleosome occupancy	Location of nucleosomes along DNA	36 bp	8	Paired	60 million

^†Longer read lengths can be used but may not provide additional gains. We find that 36 bp is sufficient to map transposition sites. Given that most ATAC-seq fragments are less than 200 bp in length, sequencing reads longer than 100 bp do not provide much additional data.

^*Index length assuming the barcodes listed in Supplementary Table 2 are used.