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Use of shorter fragments improves enrichment at the TSS. The fragment length of each read can be determined with paired-end (PE) sequencing. Use of PE sequencing instead of single-end sequencing is optional, but it provides an additional means of size selection beyond gel- or bead-based size selection. In this example, read length was determined by PE sequencing. Reads <100 bp have a higher TSS signal-to-noise ratio.
