Healthy and cancer individuals from Long-read sequencing reveals aberrant fragmentation patterns and origins of circulating DNA in cancer

Oxford Nanopore sequencing data from 61 samples described in manuscript "Long-read sequencing reveals aberrant fragmentation patterns and origins of circulating DNA in cancer"

All data are aligned to UCSC analysisSet hg38 (https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/analysisSet/), and use 0-based coordinates.

Level 2: In order to provide combined fragmentation and methylation information, Biscuit was used to create “epiBED” files (see Methods). epiBED files contain each read on a separate line, with each DNA methylation call on the read. epiBED files can be used for combined methylation/fragmentomic analysis, and are compatible with the CelFiE-ISH software that was used for cell of origin deconvolution.

Creation of Biscuit EpiBED files:Biscuit (https://huishenlab.github.io/biscuit/) v. 1.4.1-dev  was used with the command “biscuit epiread -M -b 0 -m 0 -a 0 -5 0 -3 0 -y 0.9 -L 1000000 hg38.analysisSet.fa”, where the reference is the same UCSC reference genome used for alignment. Files are available in the Zenodo repository listed in Data Availability.

Level 3: DNA methylation BED files. BED files created by modkit (see Methods) provide one line for each CpG covered, and can be used for basic DNA methylation analysis.Creation of modkit BED files:BED files were created using modkit (https://github.com/nanoporetech/modkit) v. 0.1.5 with the command “modkit pileup --cpg --combine-strands --ignore h --filter-threshold 0.9 --bedgraph".