Workflow Type: Galaxy

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
  • array containing
    • File
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

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
  • 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
strict_intersect_peaks #main/strict_intersect_peaks n/a
  • File

Version History

v0.6 (latest) Created 10th Apr 2024 at 03:01 by WorkflowHub Bot

Updated to v0.6


Frozen v0.6 c8ff689

v0.5 Created 7th Mar 2024 at 03:02 by WorkflowHub Bot

Updated to v0.5


Frozen v0.5 6e60eba

v0.4 Created 2nd Dec 2023 at 03:01 by WorkflowHub Bot

Updated to v0.4


Frozen v0.4 f0ca4bd

v0.3 Created 28th Nov 2023 at 03:01 by WorkflowHub Bot

Updated to v0.3


Frozen v0.3 5c5394e

v0.2 Created 14th Nov 2023 at 03:02 by WorkflowHub Bot

Updated to v0.2


Frozen v0.2 88fd6de

v0.1 (earliest) Created 5th Sep 2023 at 03:01 by WorkflowHub Bot

Updated to v0.1


Frozen v0.1 e95b35c
help Creators and Submitter
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  • Lucille Delisle
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Created: 5th Sep 2023 at 03:01

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