trinity NG
transcriptomics-full-de-novo/main-workflow
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flowchart TD 20["Trinotate"]; 18 -->|transdecoder_pep| 20; 21["Differential expression analysis"]; 19 -->|TPM_no_norm_gene| 21; 3 -->|output| 21; 22["Extract and cluster differentially expressed transcripts"]; 21 -->|DE_results| 22; 19 -->|norm_TMM| 22; 3 -->|output| 22; 23["Partition genes into expression clusters"]; 22 -->|rdata| 23; 1["ℹ️ Input Collection\nCollection of R2 reads"]; style 1 stroke:#2c3143,stroke-width:4px; 0["ℹ️ Input Collection\nCollection of R1 reads"]; style 0 stroke:#2c3143,stroke-width:4px; 3["ℹ️ Input Dataset\nSamples description"]; style 3 stroke:#2c3143,stroke-width:4px; 2["Describe samples"]; 5["FastQC"]; 1 -->|output| 5; 4["FastQC"]; 0 -->|output| 4; 7["MultiQC"]; 5 -->|text_file| 7; 4 -->|text_file| 7; 6["Trimmomatic"]; 0 -->|output| 6; 1 -->|output| 6; 9["FastQC"]; 6 -->|fastq_out_r2_paired| 9; 8["FastQC"]; 6 -->|fastq_out_r1_paired| 8; 11["MultiQC"]; 9 -->|text_file| 11; 8 -->|text_file| 11; 10["Trinity"]; 6 -->|fastq_out_r2_paired| 10; 6 -->|fastq_out_r1_paired| 10; 13["Build expression matrix"]; 12 -->|genes_counts_rsem| 13; 12["Align reads and estimate abundance"]; 10 -->|assembled_transcripts| 12; 6 -->|fastq_out_r2_paired| 12; 6 -->|fastq_out_r1_paired| 12; 15["Filter low expression transcripts"]; 10 -->|assembled_transcripts| 15; 13 -->|TPM_no_norm_gene| 15; 14["RNASeq samples quality check"]; 13 -->|trans_counts| 14; 3 -->|output| 14; 17["Align reads and estimate abundance"]; 15 -->|filtered| 17; 6 -->|fastq_out_r1_paired| 17; 6 -->|fastq_out_r2_paired| 17; 16["Compute contig Ex90N50 statistic and Ex90 transcript count"]; 10 -->|assembled_transcripts| 16; 13 -->|trans_counts| 16; 19["Build expression matrix"]; 17 -->|genes_counts_rsem| 19; 18["TransDecoder"]; 15 -->|filtered| 18;
Inputs
Input | Label |
---|---|
Input dataset collection | Collection of R2 reads |
Input dataset collection | Collection of R1 reads |
Input dataset | Samples description |
Outputs
From | Output | Label |
---|---|---|
toolshed.g2.bx.psu.edu/repos/iuc/trinity_run_de_analysis/trinity_run_de_analysis/2.8.4 | Differential expression analysis | |
toolshed.g2.bx.psu.edu/repos/iuc/trinity_analyze_diff_expr/trinity_analyze_diff_expr/2.8.4 | Extract and cluster differentially expressed transcripts | |
Input dataset collection | Collection of R2 reads | |
Input dataset collection | Collection of R1 reads | |
Input dataset | Samples description | |
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.2.0 | MultiQC | |
toolshed.g2.bx.psu.edu/repos/iuc/trinity/trinity/2.8.4 | Trinity | |
toolshed.g2.bx.psu.edu/repos/iuc/trinity_abundance_estimates_to_matrix/trinity_abundance_estimates_to_matrix/2.8.4 | Build expression matrix | |
toolshed.g2.bx.psu.edu/repos/iuc/trinity_samples_qccheck/trinity_samples_qccheck/2.8.4 | RNASeq samples quality check | |
toolshed.g2.bx.psu.edu/repos/iuc/transdecoder/transdecoder/3.0.1 | TransDecoder |
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 |
---|---|---|---|
2 | 5905c7785 | 2020-02-13 15:45:22 | add workflow tag |
1 | d97d1544a | 2019-04-26 08:41:44 | add primitive verson of trinity tutorial |
For Admins
Installing the workflow tools
wget https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/full-de-novo/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