Name: GGR-cwl
Owner: Duke Center for Genomic and Computational Biology
Description: CWL tools and workflows for GGR
Created: 2016-01-26 19:55:45.0
Updated: 2017-11-30 21:15:06.0
Pushed: 2017-12-06 17:32:21.0
Homepage:
null
Size: 536
Language: Python
GitHub Committers
User | Most Recent Commit | # Commits |
Other Committers
User | Email | Most Recent Commit | # Commits |
README
GGR-cwl
CWL tools and workflows associated with the Genomics of Gene Regulation (GGR) project
GGR pipelines created using the Common Workflow Language draft-3
specification.
The workflows are parametrized with values that best suit the GGR samples, but they can be easily tailored for specific needs.
For a detail User Guide to the CWL workflows, please see the wiki.
Pipelines
Steps
- 01 - Fastq QC step:
- 02 - Trimming reads step:
- 03 - Mapping step:
- 04 - Peak calling step:
- 05 - Quantification step:
Pipelines
Steps
- 01 - Mapping step:
- 02 - Peak calling step:
- 03 - Quantification step:
Pipelines
Steps
- 00 - Genome files generation for STAR and RSEM:
- 01 - Fastq QC step:
- 02 - Trimming reads step:
- 03 - Mapping step:
- 04 - Quantification step:
Pipelines
Steps
- 01 - Fastq QC step:
- 02 - Trimming reads step:
- 03 - Mapping step:
- 04 - Peak calling step:
- 05 - Quantification step:
Workflow differences legend
Depending on the experiments, there might be small differences in the workflows which will be determined by:
- All
- Type of read:
- SE: Single End reads
- PE: Paired-End reads
- ChIP-seq & DNase-seq
- Type of region targeted:
- Narrow: Narrow (also known as Point-Source) peaks. Limited region bound (e.g. TFs).
- Broad: Broad peaks. Wide region bound (e.g. Histone modifications)
- ChIP-seq only
- With or without control. If a control sample is available
-with-control
or not.
- RNA-seq only
- Strand specificity:
- Unstranded: reads are not strand-specific, is not possible to know from which DNA strand they come.
- Stranded: reads are strand-specific and can be map to the Watson and Crick strands.
- Reverse Stranded: reads come from cDNA, which switches the mapping of the forward and reverse strand.
- Custom SJDB: By default the STAR 2-pass mapping strategy is implemented in which a first pass of STAR is run to generate a large pool of novel splice junctions (referred as SJDB). These junctions are used to generate a genome index which is employed in the mapping step. However, this 2-pass strategy can be skipped, using a custom genome index Because typically this genome would be created with a precomputed SJDB, this option is denoted with
-with-sjdb
.
- ATAC-seq only
- Blacklist removal: whether or not to mask out blacklisted regions.