Plant bulk RNA-Seq workflow

transcriptomics-mirna-target-finder/main-workflow

Author(s)

version Version
3
last_modification Last updated
Jan 20, 2023
license License
None Specified, defaults to CC-BY-4.0
galaxy-tags Tags
transcriptomics
mirna
arabidopsis

Features

Tutorial
hands_on Whole transcriptome analysis of Arabidopsis thaliana

Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness purl PURL
https://gxy.io/GTN:W00242
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
output
output
output
output
output
output
output
output
trimmed_reads_single
trimmed_reads_single
text_file
text_file
trimmed_reads_single
trimmed_reads_single
text_file
text_file
output_gene_quant
output_gene_quant
output
output
output
output_reads_collapsed
output
output
text_file
text_file
output
output
output_reads_collapsed
output
output
deseq_out
miRNAsExpressed
output
miRNAsExpressed
out_file1
out_file1
out_file1
out_file1
out_file1
deseq_out
out_file1
output
out_file1
out_file1
out_file1
out_file1
output
out_file1
output
output
output
output
out_file1
ℹ️ Input Collection
Control miRNA FASTQ collection
ℹ️ Input Collection
Treated miRNA FASTQ collection
ℹ️ Input Collection
Treated mRNA FASTQ collection
ℹ️ Input Dataset
Precursor miRNA sequences
ℹ️ Input Collection
Control mRNA FASTQ collection
ℹ️ Input Dataset
Transcriptome FASTA
ℹ️ Input Dataset
Annotation GTF
ℹ️ Input Dataset
Mature miRNA sequences
ℹ️ Input Dataset
Star miRNA sequenes
FastQC
Trim Galore!
FastQC
Trim Galore!
FastQC
FastQC
Salmon quant
Salmon quant
FastQC
MiRDeep2 Mapper
Merge collections
FastQC
MiRDeep2 Mapper
Merge collections
DESeq2
MiRDeep2 Quantifier
MultiQC
Merge collections
MiRDeep2 Quantifier
MultiQC
Filter
Cut
MultiQC
Cut
Filter
Filter
DESeq2
Cut
Filter
Filter FASTA
Filter
Filter
Cut
Filter FASTA
Filter FASTA
Concatenate datasets
TargetFinder

Inputs

Input Label
Input dataset collection Control miRNA FASTQ collection
Input dataset collection Treated miRNA FASTQ collection
Input dataset collection Treated mRNA FASTQ collection
Input dataset Precursor miRNA sequences
Input dataset collection Control mRNA FASTQ collection
Input dataset Transcriptome FASTA
Input dataset Annotation GTF
Input dataset Mature miRNA sequences
Input dataset Star miRNA sequenes

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1 DESeq2
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7 MultiQC
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7 MultiQC
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7 MultiQC
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1 DESeq2
toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/2.1 Filter FASTA
cat1 Concatenate datasets
toolshed.g2.bx.psu.edu/repos/rnateam/targetfinder/targetfinder/1.7.0+galaxy1 TargetFinder

Tools

Tool Links
Cut1
Filter1
__MERGE_COLLECTION__
cat1
toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/0.14.1.2+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.3.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/2.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7 View in ToolShed
toolshed.g2.bx.psu.edu/repos/rnateam/mirdeep2_mapper/rbc_mirdeep2_mapper/2.0.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/rnateam/mirdeep2_quantifier/rbc_mirdeep2_quantifier/2.0.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/rnateam/targetfinder/targetfinder/1.7.0+galaxy1 View in ToolShed

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
7 87d458cc1 2023-01-19 17:35:35 Undo error
6 edf36428b 2022-12-01 02:42:29 Fix tutorial
5 a6636e324 2021-04-07 02:00:34 add tags and annotation to the workflow
4 a5a1a7567 2021-04-07 01:52:31 Update workflow for miRNA target identification in Arabidopsis
3 0eacaeef4 2021-03-31 12:47:36 Update workflow and include downregulated miRNAS
2 bdbe72dd2 2021-03-25 20:01:53 Fix tests workflow
1 4b406638c 2021-03-25 19:28:23 New training: miRNA target finder

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/mirna-target-finder/workflows/main_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