consensus-peaks/consensus-peaks-chip-sr
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Workflow Type: Galaxy
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Tests 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 both subsets combined. Only peaks called using a combination of both subsets which have summits intersecting the intersection of both replicates will be kept.
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| 2 rmDup SR | #main/2 rmDup SR | A collection with 2 replicates. BAM should not have duplicates |
|
| bin_size | #main/bin_size | Bin size for average of normalized coverage |
|
| effective_genome_size | #main/effective_genome_size | Used by MACS2: H. sapiens: 2700000000, M. musculus: 1870000000, D. melanogaster: 120000000, C. elegans: 90000000 |
|
Steps
| ID | Name | Description |
|---|---|---|
| 3 | count number of reads | toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2 |
| 4 | call peaks individually | toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.2.9.1+galaxy0 |
| 5 | put all nb of reads into single dataset | toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 |
| 6 | get first narrowPeak | __EXTRACT_DATASET__ |
| 7 | get second narrowPeak | __EXTRACT_DATASET__ |
| 8 | individual normalized bigwig | wig_to_bigWig |
| 9 | get min value | toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0 |
| 10 | strict overlap between peaks of both replicates | toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0+galaxy1 |
| 11 | average coverage from both replicates | toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_average/deeptools_bigwig_average/3.5.4+galaxy0 |
| 12 | convert min nb of reads to parameter | param_value_from_file |
| 13 | downsample BAM | toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2 |
| 14 | call peaks on merge | toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.2.9.1+galaxy0 |
| 15 | multiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1 |
| 16 | get merged peaks overlapping both replicates | toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0+galaxy1 |
| 17 | only keep peaks with summits overlapping intersection of both replicates | Filter1 |
| 18 | keep only columns of narrowPeak | Cut1 |
| 19 | 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 |
|
| individual_macs2_narrowPeaks | #main/individual_macs2_narrowPeaks | n/a |
|
| merged_macs2_narrowPeaks | #main/merged_macs2_narrowPeaks | n/a |
|
| multiqc_output | #main/multiqc_output | n/a |
|
| shared_narrowPeak | #main/shared_narrowPeak | n/a |
|
| strict_intersect_peaks | #main/strict_intersect_peaks | n/a |
|
Version History
v0.1 (earliest) Created 5th Sep 2023 at 03:01 by WorkflowHub Bot
Updated to v0.1
Frozen
v0.1e95b35c
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Views: 1711
Created: 5th Sep 2023 at 03:01
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Teams: Intergalactic Workflow Commission (IWC), Vertebrate Genomes Pipelines in Galaxy, iwc
Organizations: Bots, European Galaxy Team
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IWC - Intergalactic Workflow Commission
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