DNase-HS pipeline (paired-end)

  • Status: archived
Title
DNase-HS pipeline (paired-end)
Assays
DNase-seq
Description
ENCODE Uniform Processing Pipeline of DNase-seq Hypersensitive Sites for paired-end reads (DCC version 1). This pipeline inputs gzipped DNA-sequencing reads in the form of fastqs and a genome index. These fastqs come from technical replicates that are processed with bwa to generate unfiltered and filtered alignments (bam format). The filtered alignments, combined with a DNase mappability reference. More information could be found on the attached document or https://www.encodeproject.org/dnase-seq/.
Lab
ENCODE Processing Pipeline
Pipeline standards
DNase-seq Data Standards

Pipeline schematic

Documents

pipeline protocol
Description: DNase pipeline protocol for both single- and paired-end
Submitted by
Kathrina Onate
Lab
J. Michael Cherry, Stanford