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.


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


ID Name Description
3 count number of reads
4 call peaks individually
5 put all nb of reads into single dataset
6 get first narrowPeak __EXTRACT_DATASET__
7 get second narrowPeak __EXTRACT_DATASET__
8 individual normalized bigwig wig_to_bigWig
9 get min value
10 strict overlap between peaks of both replicates
11 average coverage from both replicates
12 convert min nb of reads to parameter param_value_from_file
13 downsample BAM
14 call peaks on merge
15 multiQC
16 get merged peaks overlapping both replicates
17 only keep peaks with summits overlapping intersection of both replicates Filter1
18 keep only columns of narrowPeak Cut1
19 discard duplicated lines


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
  • Lucille Delisle

Views: 1453

Created: 5th Sep 2023 at 03:01

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