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 (Dev) WorkflowHub
Launch in Tutorial Mode question
galaxy-download Download
output
output
output
output
out_pairs
out_pairs
output
out_paired_collection
output
out_paired_collection
mapped_reads
mapped_reads
output
output
output
output
output
output
output
output
alignment_ends
peak_tables
output
alignment_ends
out_file1
output
outfile
output
output
out_file1
output
output
output
outFile
output
output
outfile
output
ℹ️ Input Collection
Background
ℹ️ Input Collection
Enriched set as a paired-end reads collection
ℹ️ Input Dataset
Annotation Reference File for RCAS
ℹ️ Input Dataset
Genome Chromosome Sizes
FastQC
Cutadapt
FastQC
Cutadapt
UMI-tools extract
UMI-tools extract
RNA STAR
RNA STAR
UMI-tools deduplicate
UMI-tools deduplicate
Extract alignment ends
FastQC
PEAKachu
Merge collections
Extract alignment ends
FastQC
Sort
Text reformatting
Sort collection
Sort
Create a BedGraph of genome coverage
bedtools SlopBed
plotFingerprint
multiBamSummary
Create a BedGraph of genome coverage
Wig/BedGraph-to-bigWig
Extract Genomic DNA
Text reformatting
plotCorrelation
Wig/BedGraph-to-bigWig
MEME-ChIP
RCAS

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
  1. 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
  2. Click on galaxy-upload Import at the top-right of the screen
  3. 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”
  4. 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