Cleanup: C. auris RNA-seq featured analysis — reconcile survey tallies, fix broken references

## Summary

A close read of the _C. auris_ RNA-seq featured analysis — [_Standardizing RNA-seq Analysis of Fungal Pathogens Using BRC-Analytics and Agentic AI_](https://brc-analytics.org/learn/featured-analyses/standardizing-rnaseq-candidozyma-auris) (source: `sites/brc-analytics/docs/learn/featured-analyses/standardizing-rnaseq-candidozyma-auris.mdx`, dated 2026-01-13) — surfaced a handful of internal-consistency defects and a couple of broken references. These are almost all editorial/consistency issues, not problems with the science or the re-analysis itself, which look solid. Grouped by priority below. Line numbers refer to the source `.mdx` at the time of writing.

Thanks to the authors for a genuinely impressive piece — flagging these only so a careful reader doesn't trip over the mismatched tallies.

## High priority (internal inconsistencies / factual)

1. **Survey tallies in the body contradict Table 2.** In _Two representative studies_ (line 86) the prose says B8441 "dominates the field (14/20 published studies)" and cites "`DESeq2` in 13/20, `HISAT2` in 6/20 studies." Table 2 (lines 68–71) instead gives **B8441 12/20 (60%)**, **`DESeq2` (12)**, and **`HISAT2` (7)**. All three disagree, and not in a consistent direction (the text's B8441/DESeq2 run higher than the table while HISAT2 runs lower). The "60%" B8441 figure recurs at lines 68/74/320, so 12/20 appears to be the intended value and "14/20" the outlier. Suggest reconciling line 86 with Table 2.

2. **A third set of survey numbers adds confusion.** The Summary Statistics block (line 493) and refs #13/#30 draw on a separate **32-paper** survey with B8441 75%, `DESeq2` 68.8%, `HISAT2` 62.5% — different denominators from Table 2's 20 linked-BioProject studies. As written, a reader sees three different DESeq2 figures (12/20, 13/20, 68.8%) and two B8441 figures (60%, 75%) without a clear statement of which survey each belongs to. A sentence distinguishing the "20 studies with linked BioProjects" set from the "32-paper" survey would resolve it.

3. **Total run count is off by one.** Table 1's TOTAL row reads **27,202** runs (line 60), while Materials and Methods (line 232) and ref #10 (line 362) both say **27,201**. The Table 1 column sums to 27,202, so the Methods/ref figure looks like the one to correct.

4. **Reference #24 misexpands "BRC."** Line 454 reads "BRC-Analytics (**Bacterial and Viral Bioinformatics Resource Center** - Analytics)"—that is the BV-BRC/PATRIC name. The body itself correctly describes BRC-Analytics as developed under the NIAID-funded **Bioinformatics Resource Centers (BRCs)** program (§ BRC-Analytics). Suggest fixing the reference-entry expansion to match.

## Medium priority (broken / inconsistent links)

5. **Broken citation anchor for FPPL.** `[FPPL, 2024](#6-critical-priority-fungal-pathogen)` (line 41) does not resolve. The heading "6. Critical Priority Fungal Pathogen Designation" slugs to `#6-critical-priority-fungal-pathogen-designation` (verified against the site's `rehypeSlug` / `slugify` config); the link is missing the `-designation` suffix. The other five in-page citation anchors (#1–#5) do resolve.

6. **Santana history link inconsistent in ref #23.** Ref #23 (line 448) points to `…/h/prjna904261-final`, whereas every other reference to that history uses `…/h/prjna904261-perm` (lines 117, 119, 152, 198, 279). The `-final` variant is likely dead; suggest aligning it to `-perm`.

7. **Wang history uses two URL forms.** § Maintaining provenance links the Wang history as a raw `histories/view?id=…` (line 198), while Methods uses the `u/cartman/h/prjna1086003-perm` permalink (line 280). Both may resolve, but standardizing on one would be cleaner.

## Low priority (clarity / freshness / optional)

8. **Als5 vs ALS4112.** The results text and Fig. 4 highlight adhesin "ALS4112" (lines 178, 189), but the Wang reference summary (#2, line 304) names the two adhesins as "Als5 and Scf1." Worth confirming these refer to the same gene and that "ALS4112" isn't a typo.

9. **Self-dating catalog counts.** "currently 5,060 assemblies for 1,920 … taxa" (line 82) will drift out of date. Consider version-neutral wording (same pattern noted for the measles featured analysis).

10. **Table 1 BioProject column doesn't sum to the total.** The per-assay BioProject counts add to 247, not the stated 237 total—presumably because a project can span multiple assay types. Correct as-is, but a one-line footnote would prevent readers from reading it as an error.

11. **Optional "since publication" note on integrated AI.** The forward-looking framing—"future releases" (Figure 1B, line 98), "emerging tools like Claude Code Web" (line 212), integration as "our development priority" (line 226)—has been partly overtaken: BRC-Analytics has since shipped its integrated assistant (feature flag removed in #1527). A short note pointing readers at it could keep the outlook section current, while leaving the described methodology intact as the record of what was done.

## Note

Several of these touch authored scientific prose and reference entries, so the fixes should go through author review rather than a drive-by PR.

Start with sites/brc-analytics/docs/learn/featured-analyses/standardizing-rnaseq-candidozyma-auris.mdx and review the cited lines, tables, references, and in-page links against the issue. Reconcile the survey and run totals, correct the named references and URLs, clarify the denominators, and confirm the ALS naming before requesting author review; done means the listed inconsistencies and broken links are resolved without changing the scientific analysis.

Written by the indexing model from the issue text.