Agent
atacseq-pipeline
Execute ENCODE ATAC-seq pipeline from FASTQ to accessibility peaks with Tn5 correction, Bowtie2, and MACS2
@ammawlaView AgentData
Agent
dnaseseq-pipeline
Execute ENCODE DNase-seq pipeline from FASTQ to hotspots and footprints using BWA, Hotspot2, and HINT-ATAC
Install
> /plugin marketplace add ammawla/encode-toolkit > /plugin install encode-toolkit@ammawla
How it fires
How this agent gets triggered: by you, by Claude, or both.
- Fires itselfAuto-invocation. Claude auto-loads it when your prompt matches the work.Auto-invocation is when the right skill fires by itself at the right moment, driven by a FLOW.md router and a hook, instead of you invoking it by name. It is the difference between a skill being installed and a skill actually getting used.Read the full definition →
- You can call itInvoke it directly when you want it.
Context preview
The summary Claude sees to decide when to auto-load this agent.
Execute ENCODE DNase-seq pipeline from FASTQ to hotspots and footprints using BWA, Hotspot2, and HINT-ATAC
Agent definition
dnaseseq-pipeline.mdname: dnaseseq-pipeline description: Execute ENCODE DNase-seq pipeline from FASTQ to hotspots and footprints using BWA, Hotspot2, and HINT-ATAC
DNase-seq Pipeline Agent
You are an ENCODE DNase-seq processing specialist. Guide users through the complete pipeline:
Pipeline Stages
1. **QC & Trimming**: FastQC + adapter trimming 2. **Alignment**: BWA-MEM to GRCh38/mm10 3. **Filtering**: Remove duplicates, ENCODE blacklist v2, MAPQ >= 30 4. **Hotspot Calling**: Hotspot2 for DNase I hypersensitive sites (DHS) 5. **Footprinting**: HINT-ATAC for transcription factor footprint detection 6. **Signal Tracks**: Normalized DNase-seq signal bigWig
Quality Thresholds
- SPOT score (Signal Portion of Tags) >= 0.4
- FRiP >= 1%
- 2+ biological replicates
Output Types
- narrowPeak: DNase I hypersensitive sites
- Footprint BED: TF footprint locations
- bigWig: Normalized DNase signal
Tools
Use `encode_search_experiments` with assay_title="DNase-seq" to find data.
Refer to the pipeline-dnaseseq skill for full Nextflow implementation.
Ships withencode-toolkit
Search ENCODE, cross-reference 14 databases, run 7 analysis pipelines, and generate publication-ready methods — all from natural language in Claude Code.
Get the whole plugin
Stats
24
Stars
5
Forks
Maintained
Maintenance
Python
Language
AGPL-3.0
License
1mo ago
Last commit
6mo ago
Created
Repo: ammawla/encode-toolkit
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