# HGPS ATAC-seq feasibility — status as of 2026-05-02 evening

**Goal:** pre-submission addition for v103 — does the supra-compartment wave
attenuate in HGPS dermal fibroblasts vs age-matched controls? Tests whether
lamin A is a coherence factor (like RIF1) or a wavelength setter.

## Method validation — DONE ✓

The consecutive-peak CWT recipe (substrate (a): peak-indexed `signalValue`,
Paul m=2, $T = 4\pi s/5$) is well understood and applied. Validated against
v38 K562 canonical with byte-exact reproduction of `N_peaks`, AR(1) `α`, and
`sig95 > 5%` on 22/22 autosomes; dominant period within one log-grid step.
Full validation report: `validation/VALIDATION_RESULT.md`.

End-to-end pipeline demonstrated on pooled-control fibroblast MACS2 output:
22/22 autosomes processed, **median N_cycles = 5.30, dom_period = 25.7 Mbp** —
matches the manuscript's "N ≈ 5 cycles per chromosome" headline (Fig 2d).

## Data acquisition — bandwidth-blocked

**Confirmed** GSE150136 deposit contains only POOLED-control MACS2 narrowPeak
XLS (29,465 + 1,049 peaks); NO per-sample BEDs, NO bigWig, NO BAM. To run
the HGPS-vs-control comparison we must process the 8 raw fastq files
ourselves.

Active background downloads (started 16:55):
- bowtie2 prebuilt GRCh37 index: 412 MB / ~3.5 GB (12% complete after 14 min)
- SRR11735719 (smallest control fastq R1): 402 MB / ~10 GB (4% complete)

At the observed ~565 KB/s rate:
- bowtie2 index ETA: ~90 more minutes
- single fastq pair ETA: ~6–8 hours
- all 8 fastq pairs sequential: ~50–70 hours of download alone
- bowtie2 alignment + MACS3 peak calling per sample: 3–6 hours per sample on this M4
- **total realistic end-to-end on local machine: 3–5 days**

## Pipeline scripts — READY

| Script | Purpose | Status |
|---|---|---|
| `scripts/01_align_call_peaks.sh` | bowtie2 align → samtools dedup/filter → MACS3 callpeak → chromperiod | ✓ written, syntax OK |
| `scripts/02_run_chromperiod_per_sample.py` | substrate-(a) Paul m=2 CWT per sample | ✓ validated against v38 K562 |
| `scripts/03_aggregate_and_test.py` | mixed-effects model HGPS-vs-control + disposition | ✓ written, statsmodels installed |

## Next-step decision points

Three honest paths:

**Path A — wait for downloads.** Background `curl`s are running. Estimated
total wall-clock 3–5 days. No additional action needed; just leave the machine
on. Result will integrate into v104 (the v103 cycle is too short).

**Path B — ENA Aspera or `prefetch` re-acquisition.** SRA Toolkit's `prefetch`
typically gets 5–20 MB/s on academic networks (10–40× the current curl rate).
If `prefetch` is or can be installed locally, all 8 fastqs can complete in
6–10 hours. Proof-of-concept would then run on the youngest 4 samples
(2 controls + 2 HGPS young) within 24 hours.

**Path C — reframe the v103 contribution.** Drop the HGPS comparison from
v103, keep only the *method-validation* + *pooled-control* result as a
pre-submission methodology supplement: documents that the wave is detectable
in primary human dermal fibroblasts (not just cancer cell lines) at
$T = 26$ Mbp and $N \approx 5$ cycles per chromosome, with the full pipeline
ready for a v104 HGPS analysis once data are in hand.

## Recommendation

**Path C is the honest pre-submission move:** the method-validation and
pooled-control fibroblast result is a clean, publishable methodology
supplement that strengthens the manuscript's cross-substrate generality
claim without requiring HGPS data. The HGPS comparison itself becomes a
v104 / revision-response analysis with the pipeline pre-validated and
disposition pre-committed.

The pre-committed disposition file (`PRE_COMMITTED_DISPOSITION.md`) is locked
either way; running HGPS data through it later will not change the A/B/C
thresholds or the primary endpoint.

## Files touched this session

- `PRE_COMMITTED_DISPOSITION.md` — locked + amended with sample-count
  correction, validation result, and data-acquisition path
- `data/samples_manifest.csv` — 8 samples (6 HGPS + 2 control) from GSE150136
- `scripts/01_align_call_peaks.sh` — fastq → narrowPeak driver
- `scripts/02_run_chromperiod_per_sample.py` — chromperiod (validated)
- `scripts/03_aggregate_and_test.py` — mixed-effects model
- `validation/K562_per_chrom_summary.csv` — validation table (22 chroms)
- `validation/VALIDATION_RESULT.md` — validation report (recipe locked)
- `validation/fibroblast_control/per_chrom_summary.csv` — pooled-control end-to-end
- `validation/fibroblast_control/phase_map_500kb.csv` — pooled-control phase map
- `STATUS_2026-05-02.md` — this file
