consensus-peaks/consensus-peaks-chip-sr

This workflow takes as input SR BAM from ChIP-seq. It calls peaks on each replicate and intersect them. In parallel, each BAM is subsetted to smallest number of reads. Peaks are called using all subsets combined. Only peaks called using a combination of all subsets which have summits intersecting the intersection of at least x replicates will be kept.

Inputs

ID	Name	Description	Type
Minimum number of overlap	#main/Minimum number of overlap	Minimum number of replicates into which the summit should be present.	int
bin_size	#main/bin_size	Bin size for average of normalized coverage	int
effective_genome_size	#main/effective_genome_size	Used by MACS2: H. sapiens: 2700000000, M. musculus: 1870000000, D. melanogaster: 120000000, C. elegans: 90000000	int
n rmDup BAMSR	#main/n rmDup BAMSR	A collection with n replicates. BAM should not have duplicates	array containing File

Steps

ID	Name	Description
4	count number of reads	toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2
5	generate filter rule	toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
6	call peaks individually	toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.2.9.1+galaxy0
7	put all nb of reads into single dataset	toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
8	compute multi intersect	toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.30.0
9	individual normalized bigwig	wig_to_bigWig
10	get min value	toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0
11	get nb of replicates	wc_gnu
12	filter multi intersect	Filter1
13	average coverage from replicates	toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_average/deeptools_bigwig_average/3.5.4+galaxy0
14	convert min value to text	param_value_from_file
15	Parse parameter value	get nb of rep as param param_value_from_file
16	create a dataset with the min value as many times as there are replicates	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1
17	split min value	toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.1
18	convert min nb of reads to parameter	param_value_from_file
19	downsample BAM	toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2
20	call peaks on merge	toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.2.9.1+galaxy0
21	get merged peaks overlapping at least x replicates	toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0+galaxy1
22	multiQC	toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1
23	only keep peaks with summits overlapping intersection of at least x replicates	Filter1
24	keep only columns of narrowPeak	Cut1
25	discard duplicated lines	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/9.3+galaxy1

Outputs

ID	Name	Description	Type
average_bigwig	#main/average_bigwig	n/a	File
individual_macs2_narrowPeaks	#main/individual_macs2_narrowPeaks	n/a	File
merged_macs2_narrowPeaks	#main/merged_macs2_narrowPeaks	n/a	File
multiqc_output	#main/multiqc_output	n/a	File
shared_narrowPeak	#main/shared_narrowPeak	n/a	File

consensus-peaks/consensus-peaks-chip-sr
Version 1

Inputs

Steps

Outputs

Version History

v1.0 (earliest) Created 2nd May 2024 at 03:01 by WorkflowHub Bot

Creator

Submitter

consensus-peaks/consensus-peaks-chip-sr Version 1

Inputs

Steps

Outputs

Version History

v1.0 (earliest) Created 2nd May 2024 at 03:01 by WorkflowHub Bot

Creator

Submitter

Related items

consensus-peaks/consensus-peaks-chip-sr
Version 1