Plant bulk RNA-Seq workflow
transcriptomics-mirna-target-finder/main-workflow
Launch in Tutorial Mode
question
galaxy-download Download
galaxy-download Download
flowchart TD 0["ℹ️ Input Collection\nControl miRNA FASTQ collection"]; style 0 stroke:#2c3143,stroke-width:4px; 1["ℹ️ Input Collection\nTreated miRNA FASTQ collection"]; style 1 stroke:#2c3143,stroke-width:4px; 2["ℹ️ Input Collection\nTreated mRNA FASTQ collection"]; style 2 stroke:#2c3143,stroke-width:4px; 3["ℹ️ Input Dataset\nPrecursor miRNA sequences"]; style 3 stroke:#2c3143,stroke-width:4px; 4["ℹ️ Input Collection\nControl mRNA FASTQ collection"]; style 4 stroke:#2c3143,stroke-width:4px; 5["ℹ️ Input Dataset\nTranscriptome FASTA"]; style 5 stroke:#2c3143,stroke-width:4px; 6["ℹ️ Input Dataset\nAnnotation GTF"]; style 6 stroke:#2c3143,stroke-width:4px; 7["ℹ️ Input Dataset\nMature miRNA sequences"]; style 7 stroke:#2c3143,stroke-width:4px; 8["ℹ️ Input Dataset\nStar miRNA sequenes"]; style 8 stroke:#2c3143,stroke-width:4px; 9["FastQC"]; 0 -->|output| 9; 10["Trim Galore!"]; 0 -->|output| 10; 11["FastQC"]; 1 -->|output| 11; 12["Trim Galore!"]; 1 -->|output| 12; 13["FastQC"]; 2 -->|output| 13; 14["FastQC"]; 4 -->|output| 14; 15["Salmon quant"]; 6 -->|output| 15; 2 -->|output| 15; 5 -->|output| 15; 16["Salmon quant"]; 6 -->|output| 16; 4 -->|output| 16; 5 -->|output| 16; 17["FastQC"]; 10 -->|trimmed_reads_single| 17; 18["MiRDeep2 Mapper"]; 10 -->|trimmed_reads_single| 18; 19["Merge collections"]; 11 -->|text_file| 19; 9 -->|text_file| 19; 20["FastQC"]; 12 -->|trimmed_reads_single| 20; 21["MiRDeep2 Mapper"]; 12 -->|trimmed_reads_single| 21; 22["Merge collections"]; 13 -->|text_file| 22; 14 -->|text_file| 22; 23["DESeq2"]; 15 -->|output_gene_quant| 23; 16 -->|output_gene_quant| 23; 6 -->|output| 23; 24["MiRDeep2 Quantifier"]; 7 -->|output| 24; 3 -->|output| 24; 18 -->|output_reads_collapsed| 24; 8 -->|output| 24; 25["MultiQC"]; 19 -->|output| 25; 26["Merge collections"]; 20 -->|text_file| 26; 17 -->|text_file| 26; 27["MiRDeep2 Quantifier"]; 7 -->|output| 27; 3 -->|output| 27; 21 -->|output_reads_collapsed| 27; 8 -->|output| 27; 28["MultiQC"]; 22 -->|output| 28; 29["Filter"]; 23 -->|deseq_out| 29; 30["Cut"]; 24 -->|miRNAsExpressed| 30; 31["MultiQC"]; 26 -->|output| 31; 32["Cut"]; 27 -->|miRNAsExpressed| 32; 33["Filter"]; 29 -->|out_file1| 33; 34["Filter"]; 29 -->|out_file1| 34; 35["DESeq2"]; 32 -->|out_file1| 35; 30 -->|out_file1| 35; 36["Cut"]; 34 -->|out_file1| 36; 37["Filter"]; 35 -->|deseq_out| 37; 38["Filter FASTA"]; 36 -->|out_file1| 38; 5 -->|output| 38; 39["Filter"]; 37 -->|out_file1| 39; 40["Filter"]; 37 -->|out_file1| 40; 41["Cut"]; 40 -->|out_file1| 41; 42["Filter FASTA"]; 41 -->|out_file1| 42; 8 -->|output| 42; 43["Filter FASTA"]; 41 -->|out_file1| 43; 7 -->|output| 43; 44["Concatenate datasets"]; 43 -->|output| 44; 42 -->|output| 44; 45["TargetFinder"]; 38 -->|output| 45; 44 -->|out_file1| 45;
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
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