consensus-peaks/consensus-peaks-chip-sr
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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 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. |
|
| 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 |
|
| n rmDup BAMSR | #main/n rmDup BAMSR | A collection with n replicates. BAM should not have duplicates |
|
Steps
| ID | Name | Description |
|---|---|---|
| 4 | count number of reads | toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3 |
| 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/2.31.1 |
| 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/0.5.2 |
| 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/1.20+galaxy3 |
| 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/2.31.1+galaxy0 |
| 22 | multiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0 |
| 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 |
|
| 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 |
|
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: 4938 Downloads: 1560 Runs: 0
Created: 5th Sep 2023 at 03:01
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