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Histone-modification ChIP-seq, ATAC-seq accessibility, chromatin state, and TF binding analysis from ENCODE, Roadmap Epigenomics, ChIP-Atlas.
Passed 11 of 17 test cases with the skill, and 7 of 17 without it.
and 4 more in the full report
7 fixed7 passed either way6 still failing2 broke
Tokens, turns and time describe resource use, not a dollar price.
One of 7 test cases the skill fixed. Same model, same prompt, with and without the skill.
To confirm whether a promoter region annotated with H3K4me3 is actively initiating transcription or heterochromatic in K562 cells, which ENCODE tool function provides 15-state ChromHMM model calls?
| Checked | Without skill | With skill |
|---|---|---|
| Recommends using ENCODE_get_chromatin_state to retrieve ChromHMM annotations. | Missed | Passed |
The instructions your model reads when the skill loads.
tooluniverse-epigenomicstooluniverse-rnaseq-deseq2tooluniverse-gwas-snp-interpretationtooluniverse-variant-analysisBefore calling any tool, identify which question type you're answering. Each maps to a different tool set.
(a) Which regulatory elements exist at a locus? Use UCSC_get_encode_cCREs (region-based) or SCREEN_get_regulatory_elements (gene-based). Then check ENCODE_get_chromatin_state for ChromHMM annotation and ENCODE_search_chromatin_accessibility for ATAC-seq evidence.
(b) Which TFs bind there? Use ReMap_get_transcription_factor_binding for ChIP-seq experiments. Use jaspar_search_matrices to retrieve binding motifs and check whether the sequence disrupts a known motif.
(c) How does a variant affect regulation? Use RegulomeDB_query_variant for a scored summary. Then build multi-layer evidence: UCSC_get_encode_cCREs (is the variant in a cCRE?), GTEx_get_single_tissue_eqtls (is it an eQTL?), jaspar_search_matrices (does it disrupt a TF motif?). No single layer is sufficient — see the variant reasoning section below.
(d) What genes are regulated by an element? Use GTEx_get_single_tissue_eqtls or GTEx_query_eqtl to find genes whose expression is associated with variants in the element. Use SCREEN_get_regulatory_elements with element_type="PLS"/"pELS"/"dELS" to classify element-to-promoter relationships.
Use histone mark identity to guide tool queries and interpret results before fetching data.
test cases passed, vs 7 / 17 without
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