Fig. 5

Nucleosome footprinting in bisulfite-treated cfDNA datasets. In a direct comparison between bisulfite-treated and enzymatically converted cfDNA libraries of similar size, the nucleosome positioning is clearly apparent from the enzymatically converted cfNOMe dataset, but only barely recognizable in the bisulfite-treated dataset. This difference can be observed when analyzing all fragment lengths in aggregate (c, d) and is even more pronounced in the long fragments (a, b). e Number of reads aligning to the transcription start site ±2 kb of 8910 autosomal (+)-stranded genes. Dataset sizes were equalized to exactly 100 million aligned reads for this comparison. cfNOMe libraries cover these genomic positions twice as well compared to bisulfite-treated libraries. The merged datasets for each specified individual were used for all calculations