Assays

ENCODEfetch keeps assay-aware behavior small and explicit. Search can use any ENCODE assay title, while samplesheet export is currently mapped for the assay families below.

Supported exporter families

Family	Assay titles recognized for export
TF binding and ChIP-seq	TF ChIP-seq, ChIP-seq, Histone ChIP-seq
Transcriptome	RNA-seq, total RNA-seq, long RNA-seq, polyA plus RNA-seq, polyA minus RNA-seq, small RNA-seq
DNA accessibility	ATAC-seq, DNase-seq, snATAC-seq, FAIRE-seq, MNase-seq

ChIP-seq

ChIP-seq export includes target antibody information and matched controls.

encodefetch \
  --assay-title "TF ChIP-seq" \
  --target-label BRD4 \
  --file-type fastq \
  --metadata-only \
  --nfcore \
  --snakemake

ATAC-seq

ATAC-seq export writes case/control FASTQ samplesheets for nf-core/atacseq-style and Snakemake workflows.

encodefetch \
  --assay-title "ATAC-seq" \
  --organism "Homo sapiens" \
  --file-type fastq \
  --metadata-only \
  --nfcore

RNA-seq

RNA-seq export writes strandedness and sequencing platform fields. If strandedness is not available, exporters use auto.

encodefetch \
  --assay-title "RNA-seq" \
  --organism "Homo sapiens" \
  --file-type fastq \
  --metadata-only \
  --nfcore \
  --snakemake

Adding an assay

New assay behavior usually needs:

• An assay class under encodefetch/assays/ if normalization differs.
• An exporter under encodefetch/exporters/.
• A mapping in write_nfcore_sheet or write_snakemake_sheet.
• Tests that assert the generated samplesheet columns and representative rows.