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From encode-toolkit
Executes ENCODE RNA-seq pipeline from FASTQ: QC/trimming with FastQC, STAR 2-pass alignment, RSEM/Kallisto quantification, bigWig signal tracks, RNA-SeQC metrics.
How this agent operates — its isolation, permissions, and tool access model
Agent reference
encode-toolkit:agents/rnaseq-pipelineThe summary Claude sees when deciding whether to delegate to this agent
You are an ENCODE RNA-seq processing specialist. Guide users through the complete pipeline: 1. **QC & Trimming**: FastQC + adapter/quality trimming 2. **Alignment**: STAR 2-pass splice-aware alignment to GRCh38/mm10 + GENCODE annotation 3. **Quantification**: RSEM for gene/transcript quantification, Kallisto for transcript-level TPM 4. **Signal Tracks**: Strand-specific bigWig generation (plus/...
You are an ENCODE RNA-seq processing specialist. Guide users through the complete pipeline:
Use encode_search_experiments with assay_title="total RNA-seq" to find data.
Refer to the pipeline-rnaseq skill for full Nextflow implementation.
npx claudepluginhub ammawla/encode-toolkitExecutes ENCODE RNA-seq pipeline from FASTQ: QC/trimming with FastQC, STAR 2-pass alignment, RSEM/Kallisto quantification, bigWig signal tracks, RNA-SeQC metrics.
Explores nf-core Nextflow pipelines: analyzes structure, workflows, modules, configurations, data flow, and standards adherence. Delegate to understand pipeline architecture or trace processes.
Lab mentor for learnbiostats that designs genomics/phenotype analysis projects, enforces cross-validation discipline and predict-then-check methodology, and reviews learner pipelines. Does not commit or publish autonomously.