Tutorial CLIPseq Explorer Demultiplexed PEAKachu eCLIP Hg38

transcriptomics-clipseq/init-workflow

Author(s)

version Version
8
last_modification Last updated
Nov 28, 2022
license License
None Specified, defaults to CC-BY-4.0
galaxy-tags Tags
transcriptomics

Features

Tutorial
hands_on CLIP-Seq data analysis from pre-processing to motif detection

Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness purl PURL
https://gxy.io/GTN:W00234
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
Launch in Tutorial Mode question
galaxy-download Download
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;

Inputs

Input Label
Input dataset collection Background
Input dataset collection Enriched set as a paired-end reads collection
Input dataset Annotation Reference File for RCAS
Input dataset Genome Chromosome Sizes

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0 FastQC
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0 FastQC
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1 Cutadapt
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0 FastQC
toolshed.g2.bx.psu.edu/repos/rnateam/peakachu/peakachu/0.1.0.2 PEAKachu
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0 FastQC
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/3.5.1.0.0 plotFingerprint
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.5.1.0.0 plotCorrelation
wig_to_bigWig Wig/BedGraph-to-bigWig
toolshed.g2.bx.psu.edu/repos/iuc/meme_chip/meme_chip/4.11.2+galaxy1 MEME-ChIP
toolshed.g2.bx.psu.edu/repos/rnateam/rcas/rcas/1.5.4 RCAS

Tools

Tool Links
__MERGE_COLLECTION__
__SORTLIST__
sort1
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/text_processing/tp_awk_tool/1.1.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/bctools_extract_alignment_ends/bctools_extract_alignment_ends/0.2.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed_bedgraph/2.19.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/extract_genomic_dna/Extract genomic DNA 1/3.0.3+galaxy2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/meme_chip/meme_chip/4.11.2+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_dedup/umi_tools_dedup/1.1.2+galaxy2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/rnateam/peakachu/peakachu/0.1.0.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/rnateam/rcas/rcas/1.5.4 View in ToolShed
wig_to_bigWig

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 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

Version History

Version Commit Time Comments
8 3d3591991 2022-11-27 13:14:21 clipseq workflow.ga updated
7 5531ece3f 2022-09-28 12:56:52 clipseq workflow.ga cutadapt v1.6 -> v4.0
6 667ff3de9 2020-01-22 10:59:29 annotation
5 eb4d724e0 2020-01-15 10:41:35 Workflow renaming
4 9bd532043 2019-08-06 08:45:04 Changes to trainign workflow
3 361236c41 2019-04-04 09:00:14 Changed format of workflows
2 1951bb1a0 2019-02-13 12:03:23 Training clipseq new version (#1265)
1 b4f9079e5 2018-08-08 11:35:39 Add skeleton for clipseq tutorial

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