correlation-of-samples-on-peaks/correlation-of-samples-on-peaks
v0.1

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Workflow Type: Galaxy

This workflow computes read coverage of BAM/CRAM samples over a merged set of peak regions to generate a pairwise correlation plot, along with the corresponding raw read counts and coverage matrix.

SEEK ID: https://workflowhub.eu/workflows/2225?version=1

Inputs

ID Name Description Type
BAM or CRAM files #main/BAM or CRAM files This takes the BAM/CRAM formatted alignment files
  • array containing
    • File
Collection of peak files #main/Collection of peak files Here we are taking a collection of all peak files you wish to use.
  • array containing
    • File
Reference genome #main/Reference genome Select reference genome of your choice
  • string

Steps

ID Name Description
3 Concatenate all files into one This step concatenates multiple datasets into one toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.5+galaxy3
4 Sort bed files This sorts the bed files by chosen rules toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.31.1+galaxy0
5 Merge bed file Merges with the sorted bed file toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.31.1+galaxy2
6 multiBamSummary Computes average read coverage by counting reads from the input BAM/CRAM files over the regions defined in the sorted BED file. toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/3.5.2+galaxy0
7 Correlation plot Calculates pairwise correlations between samples using the coverage matrix generated by multiBamSummary toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.5.2+galaxy0

Outputs

ID Name Description Type
Correlation plot #main/Correlation plot n/a
  • File
deepTools coverage matrix #main/deepTools coverage matrix n/a
  • File
deepTools raw counts #main/deepTools raw counts n/a
  • File

Version History

v0.1 (earliest) Created 22nd Jul 2026 at 03:01 by WorkflowHub Bot

Updated to v0.1


Frozen v0.1 6476dc6
help Creators and Submitter
Creators
  • Lucille Delisle
  • Alexandre Mayran
  • Olusegun E. Adebayo
Submitter
License
MIT License (MIT)
Activity

Views: 2   Downloads: 1   Runs: 0

Created: 22nd Jul 2026 at 03:01

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