Workflow: Super-enhancer post ChIP-Seq analysis
Super-enhancers, consist of clusters of enhancers that are densely occupied by the master regulators and Mediator. Super-enhancers differ from typical enhancers in size, transcription factor density and content, ability to activate transcription, and sensitivity to perturbation. Use to create stitched enhancers, and to separate super-enhancers from typical enhancers using sequencing data (.bam) given a file of previously identified constituent enhancers (.gff)
- Selected
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- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Inputs
ID | Type | Title | Doc |
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alias | String | Experiment short name/Alias | |
bambai_pair | File [BAM] | Coordinate sorted BAM+BAI files |
Coordinate sorted BAM file and BAI index file |
promoter_bp | Integer (Optional) | Promoter distance |
Promoter distance for gene names assignment |
islands_file | File [xls] | XLS called peaks file |
Input XLS file generated by MACS2 |
tss_distance | Integer (Optional) | TSS distance |
Distance from TSS to exclude, 0 = no TSS exclusion |
annotation_file | File [TSV] | TSV annotation file |
TSV annotation file |
stitch_distance | Integer (Optional) | Stitching distance |
Linking distance for stitching |
chrom_length_file | File [Textual format] | Chromosome length file |
Chromosome length file |
islands_control_file | File (Optional) [xls] | XLS called peaks file (control) |
Control XLS file generated by MACS2 |
Steps
ID | Runs | Label | Doc |
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make_gff |
../tools/makegff.cwl
(CommandLineTool)
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Tool produces GFF output from the file generated by iaintersect.cwl or macs2-callpeak-biowardrobe-only.cwl tool Both islands_file and islands_control_file should be produced by the same tool |
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run_rose |
../tools/rose.cwl
(CommandLineTool)
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Tool runs ROSE to get Super Enhancers regions -b and -c arguments are not supported |
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sort_bed |
../tools/linux-sort.cwl
(CommandLineTool)
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Tool sorts data from `unsorted_file` by key |
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reduce_bed |
super-enhancer.cwl#reduce_bed/444daef3-1442-43ce-8e9c-c44d53e4427f
(CommandLineTool)
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Tool converts BED6 to BED4 by reducing column numbers |
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rename_png |
super-enhancer.cwl#rename_png/1bc95f14-0441-4994-a74d-976f7e2ac032
(CommandLineTool)
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Tool renames (copy) `source_file` to `target_filename` |
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bed_to_macs |
super-enhancer.cwl#bed_to_macs/c570e45a-f0bd-4763-818f-27cc5099bd22
(CommandLineTool)
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Tool converts `input_file` to the format compatible with the input of iaintersect from `assign_genes` step |
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assign_genes |
../tools/iaintersect.cwl
(CommandLineTool)
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Tool assigns each peak obtained from MACS2 to a gene and region (upstream, promoter, exon, intron, intergenic) |
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bed_to_bigbed |
super-enhancer.cwl#bed_to_bigbed/9e3d5bf9-c863-4084-a87c-ddaaf61f8812
(CommandLineTool)
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Tool converts bed to bigBed |
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add_island_names |
super-enhancer.cwl#add_island_names/a3ef382e-b493-4fc0-bb30-5582671be68d
(CommandLineTool)
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Outputs
ID | Type | Label | Doc |
---|---|---|---|
png_file | File [PNG] | ROSE visualization plot |
Generated by ROSE visualization plot |
bigbed_file | File [TSV] | Gateway Super Enhancer bigBed file |
Gateway Super Enhancer bigBed file |
gene_names_file | File [TSV] | Gateway Super Enhancer + gene names |
Gateway Super Enhancer results from ROSE with assigned gene names |
https://w3id.org/cwl/view/git/a68821bf3a9ceadc3b2ffbb535d601d9a645b377/workflows/super-enhancer.cwl