Workflows

These workflows are associated with CLIP-Seq data analysis from pre-processing to motif detection

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.

Tutorial CLIPseq Explorer Demultiplexed PEAKachu eCLIP Hg38

Last updated Nov 27, 2022

Launch in Tutorial Mode question
License: None Specified, defaults to CC-BY-4.0
Tests: ❌ Results: Not yet automated

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;
	

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 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