bio-atac-seq-allele-specific-accessibility skillA
bio-atac-seq-allele-specific-accessibility is agent-read markdown (skill) from pku-yuangroup/openai4s: Detect allele-specific chromatin accessibility from ATAC-seq using WASP, GATK ASEReadCounter, or RASQUAL. Use when mapping cis-regulatory genetic variants from heterozygous SNPs, separating cis from trans regulation, building chromatin QTL (caQTL) maps, validating GWAS variant function with allelic imbalance, or detecting reference allele mapping bias before downstream analysis..
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What the file says
## Version Compatibility
Reference examples tested with: WASP 0.3.4+, GATK 4.4+, RASQUAL 1.1+, samtools 1.19+, bcftools 1.19+, vcftools 0.1.16+, plink 2.00+, MatrixEQTL 2.3+, QuASAR 0.1+, bowtie2 2.5+, bwa-mem2 2.2.1+, scipy 1.11+ (false_discovery_control), pandas 2+, pybedtools 0.10+.
Verify before use:
- CLI: `<tool> --version` then `<tool> --help` to confirm flags
- Python: `pip show <package>` then `help(module.function)` to check signatures
- R: `packageVersion('<pkg>')` then `?function_name` to verify parameters
If code throws unexpected errors, introspect the installed package and adapt rather than retrying.
# Allele-Specific Accessibility
**"Does this heterozygous SNP affect chromatin accessibility on its allele?"** -> Count ATAC reads supporting reference vs alternative allele at heterozygous sites in the same individual; significant deviation from 50:50 indicates cis-regulatory effect. Requires careful handling of reference-allele mapping bias (WASP filtering) and within-individual binomial testing.
- CLI: `WASP` (Geijn 2015) for de-biased reference mapping
- CLI: `gatk ASEReadCounter` for allele-specific count tables
…Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-atac-seq-allele-specific-accessibility@git:20260821.2d1b678mdr add pku-yuangroup/openai4s/bio-atac-seq-allele-specific-accessibility@sha256:c95b0e66260b8395Pin to a label to follow the author's releases, or to a sha256 to freeze the exact bytes forever. Either way the resolved hash is written to mdr.lock, and mdr install reproduces it on any machine.
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Audit of the latest version
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Source
pku-yuangroup/openai4s · 586 stars · license MIT · pushed 2026-09-23 · branch main
API
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