Workflow: Super-enhancer post ChIP-Seq analysis

Fetched 2023-01-14 02:27:11 GMT

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)

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Inputs

ID Type Title Doc
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
make_gff
../tools/makegff.cwl (CommandLineTool)

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

run_rose
../tools/rose.cwl (CommandLineTool)

Tool runs ROSE to get Super Enhancers regions -b and -c arguments are not supported

sort_bed
../tools/linux-sort.cwl (CommandLineTool)

Tool sorts data from `unsorted_file` by key

`default_output_filename` function returns file name identical to `unsorted_file`, if `output_filename` is not provided.

reduce_bed
super-enhancer.cwl#reduce_bed/444daef3-1442-43ce-8e9c-c44d53e4427f (CommandLineTool)

Tool converts BED6 to BED4 by reducing column numbers
rename_png
super-enhancer.cwl#rename_png/1bc95f14-0441-4994-a74d-976f7e2ac032 (CommandLineTool)

Tool renames (copy) `source_file` to `target_filename`
bed_to_macs
super-enhancer.cwl#bed_to_macs/c570e45a-f0bd-4763-818f-27cc5099bd22 (CommandLineTool)

Tool converts `input_file` to the format compatible with the input of iaintersect from `assign_genes` step
assign_genes
../tools/iaintersect.cwl (CommandLineTool)

Tool assigns each peak obtained from MACS2 to a gene and region (upstream, promoter, exon, intron, intergenic)

`default_output_filename` function returns output filename with sufix set as `ext` argument. Function is called when either `output_filename` or `log_filename` inputs are not provided.

bed_to_bigbed
super-enhancer.cwl#bed_to_bigbed/9e3d5bf9-c863-4084-a87c-ddaaf61f8812 (CommandLineTool)

Tool converts bed to bigBed
add_island_names
super-enhancer.cwl#add_island_names/a3ef382e-b493-4fc0-bb30-5582671be68d (CommandLineTool)

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
html json turtle jsonld rdfxml svg png dot zip ro yaml raw
Permalink: https://w3id.org/cwl/view/git/a68821bf3a9ceadc3b2ffbb535d601d9a645b377/workflows/super-enhancer.cwl