This is a simple makefile for running the series of steps to do aligning and peak calling for DNase-seq libraries. The paired-end data should be called "R1.fq.gz" and "R2.fq.gz". Then simply run "make -f pipeline.makefile" while in the directory with your data and the makefile.
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A pipeline for aligning DNase-seq data and identifying DNase hypersensitivity sites
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