consensus-peaks/consensus-peaks-chip-sr
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Tests Identifies high-confidence consensus peaks from ChIP-seq single-end replicate experiments. The workflow calls peaks on individual replicates and identifies their intersection. To control for sequencing depth differences, it subsamples all replicates to the smallest library size, performs peak calling on the combined normalized data, and retains only peaks whose summits overlap with intersections from a user-defined minimum number of replicates.
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/1.22+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/2.31.1 |
| 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+galaxy2 |
| 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/9.5+galaxy3 |
| 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/1.22+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/2.31.1+galaxy0 |
| 22 | multiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.33+galaxy2 |
| 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/9.5+galaxy3 |
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
Creators and Submitter
Views: 14462 Downloads: 38642 Runs: 0
Created: 5th Sep 2023 at 03:01
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