Example data for IDLI analysis of nucleosome distortion

E14 mESC SAMOSA data, subsambled to 10,000 reads, in biological duplicate, for reproducing key results from Yang, Richter, and Wang et al. 2026. Starting files are forHMM, from previously published SAMOSA pipeline (GitHub - SAMOSA), aligned.ccs.bam also included for convenience. Outputs from clustering script using 100,000 nucleosomes per sample, including output plots, are included for comparison with your own results. Processing scripts, to go from forHMM to output shown here, are available on Github - IDLI and full raw data are available at GSE288933. Steps for processing example data:1. run Python script: HMMv2_IDLI_forZenodo.py (go from forHMM to HMMres and footprints)2. run interactive Jupyter notebook: IDLI_clustering_forZenodo.ipynb (performs IDLI and clustering)3. run R code: ClusterPlotting_forZenodo.Rmd (plots clustering output to visualize/group nucleosome types) The first two steps assume file paths are stored in a sample reference sheet, an example is included in this repo but make sure to adjust to match your own directories and file paths.