Workflows

These workflows are associated with Formation of the Super-Structures on the Inactive X

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.

GTN - ChIP Seq - Formation Of Super Structures On Xi
Friederike Dündar, Anika Erxleben, Bérénice Batut, Vivek Bhardwaj, Fidel Ramirez, Leily Rabbani, Pavankumar Videm

Last updated Jul 17, 2023

Launch in Tutorial Mode
License: CC-BY-4.0
Tests: ✅ Results: Not yet automated

Download Galaxy Workflow.ga Galaxy Main Galaxy Australia Galaxy France Galaxy Europe Import to another server (≥23.0+ only!) 
flowchart TD
  0["ℹ️ Input Dataset\nwt_H3K4me3_read2.fastq.gz"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nwt_H3K4me3_read1.fastq.gz"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nwt_input_rep1.bam"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nwt_H3K4me3_rep1.bam"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Dataset\nwt_CTCF_rep1.bam"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["ℹ️ Input Dataset\nwt_H3K27me3_rep1.bam"];
  style 5 stroke:#2c3143,stroke-width:4px;
  6["ℹ️ Input Dataset\nwt_input_rep2.bam"];
  style 6 stroke:#2c3143,stroke-width:4px;
  7["ℹ️ Input Dataset\nwt_H3K4me3_rep2.bam"];
  style 7 stroke:#2c3143,stroke-width:4px;
  8["ℹ️ Input Dataset\nwt_CTCF_rep2.bam"];
  style 8 stroke:#2c3143,stroke-width:4px;
  9["ℹ️ Input Dataset\nwt_H3K27me3_rep2.bam"];
  style 9 stroke:#2c3143,stroke-width:4px;
  10["FastQC"];
  0 -->|output| 10;
  892e22b2-3194-4076-af80-357530c17186["Output\nwt_H3K4me3_rep1_read2_fastqc"];
  10 --> 892e22b2-3194-4076-af80-357530c17186;
  style 892e22b2-3194-4076-af80-357530c17186 stroke:#2c3143,stroke-width:4px;
  11["Trim Galore!"];
  1 -->|output| 11;
  0 -->|output| 11;
  a66a6432-690f-4e66-88c0-7eba0a014677["Output\nwt_H3K4me3_rep1_trim_galore"];
  11 --> a66a6432-690f-4e66-88c0-7eba0a014677;
  style a66a6432-690f-4e66-88c0-7eba0a014677 stroke:#2c3143,stroke-width:4px;
  12["FastQC"];
  1 -->|output| 12;
  da453096-fdd9-44ee-b83b-e4eca5c800f9["Output\nwt_H3K4me3_rep1_read1_fastqc"];
  12 --> da453096-fdd9-44ee-b83b-e4eca5c800f9;
  style da453096-fdd9-44ee-b83b-e4eca5c800f9 stroke:#2c3143,stroke-width:4px;
  13["Samtools idxstats"];
  2 -->|output| 13;
  14["bamCoverage"];
  2 -->|output| 14;
  15["bamCoverage"];
  3 -->|output| 15;
  16["bamCoverage"];
  3 -->|output| 16;
  73e2f018-d9e4-4f74-8110-598b9b43a940["Output\nwt_H3K4me3_rep1_bamcoverage"];
  16 --> 73e2f018-d9e4-4f74-8110-598b9b43a940;
  style 73e2f018-d9e4-4f74-8110-598b9b43a940 stroke:#2c3143,stroke-width:4px;
  17["Samtools idxstats"];
  3 -->|output| 17;
  09449d6f-ce88-4448-9928-064c729c32d1["Output\nwt_H3K4me3_rep1_idxstats"];
  17 --> 09449d6f-ce88-4448-9928-064c729c32d1;
  style 09449d6f-ce88-4448-9928-064c729c32d1 stroke:#2c3143,stroke-width:4px;
  18["plotFingerprint"];
  3 -->|output| 18;
  2 -->|output| 18;
  19["bamCompare"];
  3 -->|output| 19;
  2 -->|output| 19;
  20["MACS2 callpeak"];
  2 -->|output| 20;
  3 -->|output| 20;
  a36b5a6c-d992-4a2d-8fd8-95e8eac74cbd["Output\nwt_H3K4me3_input_rep1_macs2"];
  20 --> a36b5a6c-d992-4a2d-8fd8-95e8eac74cbd;
  style a36b5a6c-d992-4a2d-8fd8-95e8eac74cbd stroke:#2c3143,stroke-width:4px;
  21["bamCompare"];
  3 -->|output| 21;
  2 -->|output| 21;
  5174d1aa-21f6-4187-8935-70ba8bd0f6e0["Output\nwt_H3K4me3_input_rep1_bamcompare"];
  21 --> 5174d1aa-21f6-4187-8935-70ba8bd0f6e0;
  style 5174d1aa-21f6-4187-8935-70ba8bd0f6e0 stroke:#2c3143,stroke-width:4px;
  22["bamCompare"];
  4 -->|output| 22;
  2 -->|output| 22;
  23["MACS2 callpeak"];
  2 -->|output| 23;
  4 -->|output| 23;
  24["bamCompare"];
  4 -->|output| 24;
  2 -->|output| 24;
  25["bamCompare"];
  5 -->|output| 25;
  2 -->|output| 25;
  26["MACS2 callpeak"];
  2 -->|output| 26;
  5 -->|output| 26;
  27["bamCompare"];
  7 -->|output| 27;
  6 -->|output| 27;
  28["MACS2 callpeak"];
  6 -->|output| 28;
  7 -->|output| 28;
  29["bamCompare"];
  8 -->|output| 29;
  6 -->|output| 29;
  30["MACS2 callpeak"];
  6 -->|output| 30;
  8 -->|output| 30;
  31["multiBamSummary"];
  2 -->|output| 31;
  3 -->|output| 31;
  4 -->|output| 31;
  5 -->|output| 31;
  6 -->|output| 31;
  7 -->|output| 31;
  8 -->|output| 31;
  9 -->|output| 31;
  32["bamCompare"];
  9 -->|output| 32;
  6 -->|output| 32;
  33["MACS2 callpeak"];
  6 -->|output| 33;
  9 -->|output| 33;
  34["Bowtie2"];
  11 -->|trimmed_reads_pair1| 34;
  11 -->|trimmed_reads_pair2| 34;
  4c3ca5b1-2298-4bb4-8d2f-f62619f35158["Output\nwt_H3K4me3_rep1_bowtie2"];
  34 --> 4c3ca5b1-2298-4bb4-8d2f-f62619f35158;
  style 4c3ca5b1-2298-4bb4-8d2f-f62619f35158 stroke:#2c3143,stroke-width:4px;
  35["Concatenate datasets"];
  20 -->|output_narrowpeaks| 35;
  23 -->|output_narrowpeaks| 35;
  36["plotCorrelation"];
  31 -->|outFile| 36;
  37["Concatenate datasets"];
  20 -->|output_narrowpeaks| 37;
  23 -->|output_narrowpeaks| 37;
  26 -->|output_narrowpeaks| 37;
  28 -->|output_narrowpeaks| 37;
  30 -->|output_narrowpeaks| 37;
  33 -->|output_narrowpeaks| 37;
  38["bedtools SortBED"];
  35 -->|out_file1| 38;
  39["bedtools SortBED"];
  37 -->|out_file1| 39;
  40["bedtools MergeBED"];
  38 -->|output| 40;
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  41["bedtools MergeBED"];
  39 -->|output| 41;
  9c4c5a1f-f2c1-4e83-b1f9-ff32ee48baeb["Output\nwt_all_mergebed"];
  41 --> 9c4c5a1f-f2c1-4e83-b1f9-ff32ee48baeb;
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  42["computeMatrix"];
  19 -->|outFileName| 42;
  22 -->|outFileName| 42;
  40 -->|output| 42;
  43["computeMatrix"];
  19 -->|outFileName| 43;
  22 -->|outFileName| 43;
  25 -->|outFileName| 43;
  27 -->|outFileName| 43;
  29 -->|outFileName| 43;
  32 -->|outFileName| 43;
  41 -->|output| 43;
  44["plotHeatmap"];
  42 -->|outFileName| 44;
  45["plotHeatmap"];
  43 -->|outFileName| 45;

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 Workflow on the top menu bar of Galaxy. You will see a list of all your workflows.
  • Click on 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