atac-timing

Code to run ATAC analysis benchmarks

• atac-timing/merge-fragments:
  • Merge genome-sorted fragments data from multiple files (i.e. one per sample) into a single sorted file
  • Requires: datasets/atac-process
  • Produces:
    • {RESULTS_ROOT}/raw/atac-timing/merge-fragments: Raw timing outputs
    • {RESULTS_ROOT}/data_tables/atac-timing/merge-fragments.tsv
  • Figures: Fig S3c
  • Task summary: 40/40 completed. Total time: 23:25:45
• atac-timing/peak-tile-timing
  • Peak and tile matrix creation benchmark
  • Requires: datasets/atac-process
  • Produces:
    • {DATA_ROOT}/atac/{dataset}/peak-subsets/: Peak sets used for benchmarking
    • {RESULTS_ROOT}/raw/atac-timing/peak-tile-timing/: Raw timing outputs
    • {RESULTS_ROOT}/data_tables/atac-timing/peak-tile-timing.tsv.gz
  • Figures: Fig 1e-g, Fig S1 e+f
  • Task summary: 520/520 completed. Total time: 6 days, 17:06:59