ENCODE DNase Uniform Processing Pipeline - Version 2.1.2

This minor revision of the ENCODE DNase Uniform Processing Pipeline supersedes and invalidates v2.1 and v2.1.1. Changes over v2.0 are only in the hotspot calling step:

• Hotspot2 v2.1.1 is incorporated, which primarily increases FDR precision on the 'enrichment' (aka 'all_calls') file, which does have a positive effect on how hotspots and peaks are called.
• The 'dnase_call_hostpots' step now pre-filters the input bam and mappability files to the 1-22+XY chromosomes. The option exists to include chrM and scaffolds, though ENCODE uses the default of excluding them.
• The 'dnase_call_hotspots' step now uses bedops v2.4.33. (Other steps continue to use v2.4.19.)
• All applets are now set run on ubuntu 14.04 in DX.

ENCODE DNase Uniform Processing Pipeline - Version 2.0

This is the second major version of the ENCODE DNase Uniform Processing Pipeline. Results from this version should replace all prior results except for bwa SE alignments. A number of corrections and improvements have been made over the previous major and minor versions, which include but are not limited to:

• PE alignment parameters for bwa have been corrected.
• Now using Hotspot2 v2.0 which includes improvements and corrections.
• Now preserving hotspots "all calls" for downstream analysis.
• Normalized density generation corrected.
• Now using picard 2.8.1, which is UMI aware.
• Hotspot1 v4.1.1 SPOT scoring on a sample of the filtered reads has been added.

ENCODE DNase Uniform Processing Pipeline - Version 1.3

This release includes the supplementary applet dnase-qc-hotspot1 which will calculate the HotSpot1 (v5) score on the bam sample produced by dnase-eval-bam. Eventually these 2 steps will be collapsed into one single step. However, it is necessary to add this hotspot1 standalone step now in order to backfill the SPOT score to previously run ENCODE experiments.

ENCODE DNase Uniform Processing Pipeline - Version 1.2

This release differs only slightly from release 1.1. It includes the ability to trim fastq reads by length before single-end alignment. It also includes minor scripting improvements such as better file naming when a large number of fastq files are concatenated before alignment.

ENCODE DNase Uniform Processing Pipeline - Version 1.1

This is an official release of the ENCODE DNase uniform processing pipeline. It differs from the 1.0.x branch by the use of bwa-0.7.12. All GRCh38 and mm10 ENCODE production processing will use this release or later.

ENCODE DNase Uniform Processing Pipeline - Version 1.0.1

This is a minor revision to the first official release of the pipeline. It was necessary to reduce the samtools memory parameter due oom failures and does not change the basic processing in any way. The ENCODE DNase uniform processing pipeline is running on DNANexus in production. It features the first official release of hotspot2, and was developed in coordination with the UW Stam lab.

ENCODE DNase Uniform Processing Pipeline - Version 1.0

This is the first official release of the pipeline. The ENCODE DNase uniform processing pipeline is now running on DNANexus in production. It features the first official release of hotspot2, and was developed in coordination with the UW Stam lab.