Tutorial CLIPseq Explorer Demultiplexed PEAKachu eCLIP Hg38

Run Workflow in Galaxy

• Galaxy Europe
• Galaxy Australia
• Galaxy Main
• Galaxy France
• Import to another server (≥23.0+ only!)

flowchart TD
  0["ℹ️ Input Collection\nBackground"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Collection\nEnriched set as a paired-end reads collection"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nAnnotation Reference File for RCAS"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nGenome Chromosome Sizes"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["FastQC"];
  0 -->|output| 4;
  5["Cutadapt"];
  0 -->|output| 5;
  6["FastQC"];
  1 -->|output| 6;
  7["Cutadapt"];
  1 -->|output| 7;
  8["UMI-tools extract"];
  5 -->|out_pairs| 8;
  9["UMI-tools extract"];
  7 -->|out_pairs| 9;
  10["RNA STAR"];
  2 -->|output| 10;
  8 -->|out_paired_collection| 10;
  11["RNA STAR"];
  2 -->|output| 11;
  9 -->|out_paired_collection| 11;
  12["UMI-tools deduplicate"];
  10 -->|mapped_reads| 12;
  13["UMI-tools deduplicate"];
  11 -->|mapped_reads| 13;
  14["Extract alignment ends"];
  12 -->|output| 14;
  15["FastQC"];
  12 -->|output| 15;
  16["PEAKachu"];
  12 -->|output| 16;
  13 -->|output| 16;
  17["Merge collections"];
  12 -->|output| 17;
  13 -->|output| 17;
  18["Extract alignment ends"];
  13 -->|output| 18;
  19["FastQC"];
  13 -->|output| 19;
  20["Sort"];
  14 -->|alignment_ends| 20;
  21["Text reformatting"];
  16 -->|peak_tables| 21;
  22["Sort collection"];
  17 -->|output| 22;
  23["Sort"];
  18 -->|alignment_ends| 23;
  24["Create a BedGraph of genome coverage"];
  20 -->|out_file1| 24;
  25["bedtools SlopBed"];
  3 -->|output| 25;
  21 -->|outfile| 25;
  26["plotFingerprint"];
  22 -->|output| 26;
  27["multiBamSummary"];
  22 -->|output| 27;
  28["Create a BedGraph of genome coverage"];
  23 -->|out_file1| 28;
  29["Wig/BedGraph-to-bigWig"];
  24 -->|output| 29;
  30["Extract Genomic DNA"];
  25 -->|output| 30;
  31["Text reformatting"];
  25 -->|output| 31;
  32["plotCorrelation"];
  27 -->|outFile| 32;
  33["Wig/BedGraph-to-bigWig"];
  28 -->|output| 33;
  34["MEME-ChIP"];
  30 -->|output| 34;
  35["RCAS"];
  31 -->|outfile| 35;
  2 -->|output| 35;

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

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 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:

Version History

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/clipseq/workflows/init_workflow.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