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bulkrna-geneid-mapping

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Load when converting gene identifiers between Ensembl, Entrez, and HGNC symbol in a bulk RNA-seq count matrix. Skip if the input is already in the desired identifier system, for organisms outside human/mouse, or for non-bulk-counts inputs.

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bulkrna-geneid-mapping

When to use

Run between counting and downstream analysis when the gene identifiers in your count matrix don't match the namespace of your downstream tool (e.g. STARsolo gives Ensembl IDs but GSEA wants HGNC symbols). Currently supports Ensembl ↔ Entrez ↔ HGNC symbol for human and mouse via built-in tables, with optional mygene API enrichment. UniProt is not supported — feed via --mapping-file if needed.

Inputs & Outputs

InputFormatRequired
Count matrix.csv (gene id col + sample count cols)yes (or --demo)
Custom mapping--mapping-file TSVoptional, overrides built-ins
OutputPathNotes
Mapped matrixtables/mapped_counts.csvsame shape, gene column rewritten
Mapping tabletables/mapping_table.csvoriginal_id → target_id audit
Unmapped IDstables/unmapped_genes.csvoriginal IDs that couldn't be resolved
Reportreport.md + result.jsonsummary keys: n_original_genes, n_mapped, n_unmapped, pct_mapped, n_duplicates_resolved, duplicate_strategy, n_final_genes, from_type, to_type, species

Flow

  1. Load count matrix.
  2. Strip Ensembl version suffixes (bulkrna_geneid_mapping.py:78: ENSG00000141510.12 → ENSG00000141510).
  3. Look up each ID in the built-in mapping table; fall back to the mygene API if available (:88 warns and skips API path if mygene not importable).
  4. Resolve duplicate-target collisions per --on-duplicate (sum / first / drop).
  5. Write tables/mapped_counts.csv, tables/mapping_table.csv, tables/unmapped_genes.csv.

Gotchas

  • mygene API is opt-in via package install, not a CLI flag. bulkrna_geneid_mapping.py:88 falls back silently when mygene is not importable, leaving you with built-in-table coverage only. The summary dict does not record whether the API was used; the only signal is the warning log line and the pct_mapped value (built-in tables cover ~20 well-known cancer-relevant genes — anything substantially higher implies the API ran).
  • --from/--to only accept ensembl, entrez, symbol (bulkrna_geneid_mapping.py:271-274). UniProt and other namespaces are not in the choices list and will fail at argparse. If you need UniProt, supply a custom --mapping-file TSV.
  • Built-in tables cover human + mouse only (--species choices at :275). Other organisms fail with empty mappings if mygene isn't installed; either install mygene or supply --mapping-file.
  • Many-to-one collapses follow --on-duplicate (default sum). Default sums read counts across genes mapping to the same target symbol — meaningful for paralog families but wrong if you wanted per-isoform tracking. Choose first to take the first hit, or drop to keep only unique mappings. The number resolved is in result.json["n_duplicates_resolved"].
  • Ensembl version stripping is unconditional (:78). If your downstream tool requires the version suffix (rare), this skill silently drops it.

Key CLI

python omicsclaw.py run bulkrna-geneid-mapping --demo
python omicsclaw.py run bulkrna-geneid-mapping \
  --input counts.csv --output results/ \
  --from ensembl --to symbol --species human
python omicsclaw.py run bulkrna-geneid-mapping \
  --input counts.csv --output results/ \
  --from ensembl --to symbol --on-duplicate first

See also

  • references/parameters.md — every CLI flag and tuning hint
  • references/methodology.md — built-in tables, mygene fallback, version-suffix stripping
  • references/output_contract.md — exact output directory layout
  • Adjacent skills: bulkrna-qc (run before to inspect raw IDs), bulkrna-de (downstream — DE expects whatever ID system the rest of your pipeline uses), bulkrna-enrichment (downstream — enrichment requires HGNC symbols or Entrez IDs in most cases)