dafseq-smk
A Snakemake pipeline for DAF-seq (deaminase-assisted footprinting) data. Takes raw sequencing reads to per-haplotype chromatin accessibility tracks ready to load into a genome browser.
dafseq-smk is a reproducible Snakemake workflow for processing DAF-seq experiments. DAF-seq uses a DNA deaminase to footprint protein–DNA interactions, and the analytical challenge is turning noisy, allele-mixed reads into clean, interpretable accessibility signal.
The Endpoint
The pipeline’s output is a per-haplotype accessibility track — signal separated by allele — that drops directly into a genome browser (IGV, UCSC) for visual inspection. Phasing the signal makes allele-specific accessibility differences legible instead of averaged away.
Technical Approach
The workflow is built with Snakemake so each stage — read QC, alignment, deaminase-edit calling, haplotype phasing, and track generation — is a declared rule with explicit inputs and outputs. That makes runs reproducible, resumable after failure, and portable across a laptop or an HPC scheduler without changing the analysis logic.
Status
Working pipeline, in active development.