bio-atac-seq-allele-specific-accessibility
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.
npx skills add BioTender-max/awesome-bio-agent-skills --skill allele-specific-accessibility --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## 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+. 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 - CLI: `RASQUAL` (Kumasaka 2016) for joint cis-mapping with allelic counts - R: `QuASAR` (Harvey 2015) for genotype + ASE
- Version Compatibility
- Algorithmic Taxonomy
- Reference Allele Mapping Bias (The Single Most Important Issue)
- Per-Tool Failure Modes
- GATK ASEReadCounter without WASP -- Reference bias
- Sample size for ASE per SNP
- RASQUAL -- LD computation requirement
- WASP -- Phased vs unphased genotypes
- Cohort-level caQTL without allelic info
- Read-deep peak coverage required
- Decision Tree by Setting
- Cohort caQTL Pipeline
- Within-Peak ASE Aggregation
- RASQUAL Joint Modeling
WASP read-correction pipeline (Geijn 2015) python $WASP_DIR/mapping/find_intersecting_snps.py \ bowtie2 -x hg38_idx -1 wasp_out/$SAMPLE.remap.fq1.gz \ samtools view -bS wasp_out/$SAMPLE.remap.sam | samtools sort -o wasp_out/$SAMPLE.remap.bam samtools index wasp_out/$SAMPLE.remap.bam python $WASP_DIR/mapping/filter_remapped_reads.py \ samtools merge $OUT \ After WASP filtering, GATK ASEReadCounter is safe gatk ASEReadCounter \ for sample in $(cat samples.txt); do
What does the bio-atac-seq-allele-specific-accessibility skill do?
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.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill allele-specific-accessibility --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.