ENCODE Uniform Processing Pipeline for DNaseHS experiments.
Enables running on DNANexus but each step is available as a stand alone (DNANexus and ENCODE independent) script.
Steps:
- Preparation: bwa indexing and hotspot mappability/blacklist preparation (run once on reference files)
- stand-alone script: dnanexus/dnase-index-bwa/resources/usr/bin/dnase_index_bwa.sh
- Alignment by bwa
- paired-end script: dnanexus/dnase-align-bwa-pe/resources/usr/bin/dnase_align_bwa_pe.sh
- single-end script: dnanexus/dnase-align-bwa-se/resources/usr/bin/dnase_align_bwa_se.sh
- Merging and Filtering of bams and QC analysis
- paired-end script: dnanexus/dnase-filter-pe/resources/usr/bin/dnase_filter_pe.sh
- single-end script: dnanexus/dnase-filter-se/resources/usr/bin/dnase_filter_se.sh
- BAM evaluation script
- script: dnanexus/dnase-eval-bam/resources/usr/bin/dnase_eval_bam.sh
- Peak/hotspot calling by hotspot
- script: dnanexus/dnase-call-hotspots/resources/usr/bin/dnase_hotspot.sh
- Replicate Concordance
- script: dnanexus/dnase-rep-corr/resources/usr/bin/dnase_rep_corr.sh
Further detail and basic workflows can be seen in dnanexus/Readme.md. Most dependencies for the above scripts are contained in the same bin directories as the scripts.
There are tools to help set up a DNANexus project with these scripts:
- dnanexus/build_applets will build the applets into the named project
- This script will copy in common tools used by all steps and found in the dnanexus/tools directory
- Note that there are separate paired/single end versions of the pipelines and common steps be created distinct versions.
- dnanexus/dnaseLaunch.py can be used to build template workflows. However, it is dependent upon