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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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| name | bulkrna-geneid-mapping |
| description | 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. |
| version | 0.3.0 |
| author | OmicsClaw |
| license | MIT |
| tags | ["bulkrna","gene-id","mapping","Ensembl","Entrez","HGNC","annotation"] |
| requires | ["numpy","pandas"] |
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.
| Input | Format | Required |
|---|---|---|
| Count matrix | .csv (gene id col + sample count cols) | yes (or --demo) |
| Custom mapping | --mapping-file TSV | optional, overrides built-ins |
| Output | Path | Notes |
|---|---|---|
| Mapped matrix | tables/mapped_counts.csv | same shape, gene column rewritten |
| Mapping table | tables/mapping_table.csv | original_id → target_id audit |
| Unmapped IDs | tables/unmapped_genes.csv | original IDs that couldn't be resolved |
| Report | report.md + result.json | summary keys: n_original_genes, n_mapped, n_unmapped, pct_mapped, n_duplicates_resolved, duplicate_strategy, n_final_genes, from_type, to_type, species |
bulkrna_geneid_mapping.py:78: ENSG00000141510.12 → ENSG00000141510).:88 warns and skips API path if mygene not importable).--on-duplicate (sum / first / drop).tables/mapped_counts.csv, tables/mapping_table.csv, tables/unmapped_genes.csv.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.--species choices at :275). Other organisms fail with empty mappings if mygene isn't installed; either install mygene or supply --mapping-file.--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"].:78). If your downstream tool requires the version suffix (rare), this skill silently drops it.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
references/parameters.md — every CLI flag and tuning hintreferences/methodology.md — built-in tables, mygene fallback, version-suffix strippingreferences/output_contract.md — exact output directory layoutbulkrna-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)