GTN - ChIP Seq - Formation Of Super Structures On Xi

epigenetics-formation_of_super-structures_on_xi/formation-of-super-structures-on-xi

Author(s)
Friederike Dündar, Anika Erxleben, Bérénice Batut, Vivek Bhardwaj, Fidel Ramirez, Leily Rabbani, Pavankumar Videm, Tristan Reynolds
Version
6
Last updated
Dec 18, 2025
License
CC-BY-4.0
Tags

epigenetics

Features

Includes a Galaxy Workflow Report

Tutorial
Formation of the Super-Structures on the Inactive X

Workflow Testing
Tests: ✅
Results: Not yet automated

FAIRness PURL
https://gxy.io/GTN:W00068

Download Workflow RO-Crate

View on WorkflowHub

Launch in Tutorial Mode
Download

flowchart TD
  0["ℹ️ Input Collection\nInput Paired End Reads Collection"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nwt_input_rep1.bam"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nwt_H3K4me3_rep1.bam"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nwt_CTCF_rep1.bam"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Dataset\nwt_H3K27me3_rep1.bam"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["ℹ️ Input Dataset\nwt_input_rep2.bam"];
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  6["ℹ️ Input Dataset\nwt_H3K4me3_rep2.bam"];
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  8["ℹ️ Input Dataset\nwt_H3K27me3_rep2.bam"];
  style 8 stroke:#2c3143,stroke-width:4px;
  9["Trim Galore!"];
  0 -->|output| 9;
  a66a6432-690f-4e66-88c0-7eba0a014677["Output\nwt_H3K4me3_rep1_trim_galore"];
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  style a66a6432-690f-4e66-88c0-7eba0a014677 stroke:#2c3143,stroke-width:4px;
  10["Flatten collection"];
  0 -->|output| 10;
  11["Samtools idxstats"];
  1 -->|output| 11;
  12["bamCoverage"];
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  13["bamCoverage"];
  2 -->|output| 13;
  14["bamCoverage"];
  2 -->|output| 14;
  73e2f018-d9e4-4f74-8110-598b9b43a940["Output\nwt_H3K4me3_rep1_bamcoverage"];
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  style 73e2f018-d9e4-4f74-8110-598b9b43a940 stroke:#2c3143,stroke-width:4px;
  15["Samtools idxstats"];
  2 -->|output| 15;
  09449d6f-ce88-4448-9928-064c729c32d1["Output\nwt_H3K4me3_rep1_idxstats"];
  15 --> 09449d6f-ce88-4448-9928-064c729c32d1;
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  16["plotFingerprint"];
  2 -->|output| 16;
  1 -->|output| 16;
  17["bamCompare"];
  2 -->|output| 17;
  1 -->|output| 17;
  18["MACS2 callpeak"];
  1 -->|output| 18;
  2 -->|output| 18;
  a36b5a6c-d992-4a2d-8fd8-95e8eac74cbd["Output\nwt_H3K4me3_input_rep1_macs2"];
  18 --> a36b5a6c-d992-4a2d-8fd8-95e8eac74cbd;
  style a36b5a6c-d992-4a2d-8fd8-95e8eac74cbd stroke:#2c3143,stroke-width:4px;
  19["bamCompare"];
  2 -->|output| 19;
  1 -->|output| 19;
  5174d1aa-21f6-4187-8935-70ba8bd0f6e0["Output\nwt_H3K4me3_input_rep1_bamcompare"];
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  20["bamCompare"];
  3 -->|output| 20;
  1 -->|output| 20;
  21["MACS2 callpeak"];
  1 -->|output| 21;
  3 -->|output| 21;
  22["bamCompare"];
  3 -->|output| 22;
  1 -->|output| 22;
  23["bamCompare"];
  4 -->|output| 23;
  1 -->|output| 23;
  24["MACS2 callpeak"];
  1 -->|output| 24;
  4 -->|output| 24;
  25["bamCompare"];
  6 -->|output| 25;
  5 -->|output| 25;
  26["MACS2 callpeak"];
  5 -->|output| 26;
  6 -->|output| 26;
  27["bamCompare"];
  7 -->|output| 27;
  5 -->|output| 27;
  28["MACS2 callpeak"];
  5 -->|output| 28;
  7 -->|output| 28;
  29["multiBamSummary"];
  1 -->|output| 29;
  2 -->|output| 29;
  3 -->|output| 29;
  4 -->|output| 29;
  5 -->|output| 29;
  6 -->|output| 29;
  7 -->|output| 29;
  8 -->|output| 29;
  30["bamCompare"];
  8 -->|output| 30;
  5 -->|output| 30;
  31["MACS2 callpeak"];
  5 -->|output| 31;
  8 -->|output| 31;
  32["Bowtie2"];
  9 -->|trimmed_reads_paired_collection| 32;
  33["FastQC"];
  10 -->|output| 33;
  549b52d6-cce1-42d9-80b5-e9934913045b["Output\ntext_file"];
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  34["Concatenate datasets"];
  18 -->|output_narrowpeaks| 34;
  21 -->|output_narrowpeaks| 34;
  35["plotCorrelation"];
  29 -->|outFile| 35;
  36["Concatenate datasets"];
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  37["bedtools SortBED"];
  34 -->|out_file1| 37;
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  36 -->|out_file1| 38;
  39["bedtools MergeBED"];
  37 -->|output| 39;
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  40["bedtools MergeBED"];
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  30 -->|outFileName| 42;
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  43["plotHeatmap"];
  41 -->|outFileName| 43;
  44["plotHeatmap"];
  42 -->|outFileName| 44;

Inputs

Input	Label
Input dataset collection	Input Paired End Reads Collection
Input dataset	wt_input_rep1.bam
Input dataset	wt_H3K4me3_rep1.bam
Input dataset	wt_CTCF_rep1.bam
Input dataset	wt_H3K27me3_rep1.bam
Input dataset	wt_input_rep2.bam
Input dataset	wt_H3K4me3_rep2.bam
Input dataset	wt_CTCF_rep2.bam
Input dataset	wt_H3K27me3_rep2.bam

Outputs

From	Output	Label
toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.7+galaxy0	Trim Galore!
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.5.1.0.0	bamCoverage
toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.4	Samtools idxstats
toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.2.7.1+galaxy0	MACS2 callpeak
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/3.5.1.0.0	bamCompare
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1	FastQC
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.30.0	bedtools MergeBED
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.30.0	bedtools MergeBED

Tools

Tool	Links
__FLATTEN__
cat1
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/3.5.1.0.0	View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.5.1.0.0	View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.5.1.0.0	View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/3.5.1.0.0	View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.5.1.0.0	View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/3.5.1.0.0	View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.5.1.0.1	View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.7+galaxy0	View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.4+galaxy0
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1	View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.4	View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.30.0	View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0+galaxy2	View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.2.7.1+galaxy0	View in ToolShed

To use these workflows in Galaxy you can either click the links to download the workflows, or you can right-click and copy the link to the workflow which can be used in the Galaxy form to import workflows.

Importing into Galaxy

Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them!

Hands On: Importing a workflow

Click on galaxy-workflows-activity Workflows in the Galaxy activity bar (on the left side of the screen, or in the top menu bar of older Galaxy instances). You will see a list of all your workflows

Click on galaxy-upload Import at the top-right of the screen

Provide your workflow

Option 1: Paste the URL of the workflow into the box labelled “Archived Workflow URL”

Option 2: Upload the workflow file in the box labelled “Archived Workflow File”

Click the Import workflow button

Below is a short video demonstrating how to import a workflow from GitHub using this procedure:

Video: Importing a workflow from URL

Version History

Version	Commit	Time	Comments
9	bec47c37a	2025-12-11 23:47:56	Correct creator names
8	3c7c7588e	2025-12-11 02:12:29	Update workflow and workflow tests
7	55233fdd5	2023-07-17 13:47:25	Add licence and update author ids
6	9875d8031	2023-07-17 12:32:50	Update ChIP-Seq tutorial with latest tool versions and links
5	667ff3de9	2020-01-22 10:59:29	annotation
4	eb4d724e0	2020-01-15 10:41:35	Workflow renaming
3	a2af3178a	2020-01-13 12:49:19	GTN - ChIP-Seq - formation_of_super
2	ca7c701bf	2020-01-13 10:36:55	formation_of_super_structures_on_xi.ga
1	7e63a811a	2019-09-12 08:26:50	Move chip-seq tutorials to epigenetics topic

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/formation_of_super-structures_on_xi/workflows/formation_of_super_structures_on_xi.ga -O workflow.ga
workflow-to-tools -w workflow.ga -o tools.yaml
shed-tools install -g GALAXY -a API_KEY -t tools.yaml
workflow-install -g GALAXY -a API_KEY -w workflow.ga --publish-workflows