DNase-HS pipeline (paired-end)
- Status
- archived
- Title
- DNase-HS pipeline (paired-end)
- Assays
- DNase-seq, genetic modification followed by 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
- Award PI
- J. Michael Cherry, Stanford
- 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
- Grant
- U41HG006992