trinity NG

transcriptomics-full-de-novo/main-workflow

Author(s)

version Version
1
last_modification Last updated
Feb 13, 2020
license License
None Specified, defaults to CC-BY-4.0
galaxy-tags Tags
transcriptomics

Features

Tutorial
hands_on De novo transcriptome assembly, annotation, and differential expression analysis

Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness purl PURL
https://gxy.io/GTN:W00237
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
  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

Tool Links
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.69 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/describe_samples/describe_samples/2.8.4 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.2.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/transdecoder/transdecoder/3.0.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/trinity/trinity/2.8.4 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/trinity_abundance_estimates_to_matrix/trinity_abundance_estimates_to_matrix/2.8.4 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/trinity_align_and_estimate_abundance/trinity_align_and_estimate_abundance/2.8.4 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/trinity_analyze_diff_expr/trinity_analyze_diff_expr/2.8.4 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/trinity_contig_exn50_statistic/trinity_contig_exn50_statistic/2.8.4 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/trinity_define_clusters_by_cutting_tree/trinity_define_clusters_by_cutting_tree/2.8.4 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/trinity_filter_low_expr_transcripts/trinity_filter_low_expr_transcripts/2.8.4 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/trinity_run_de_analysis/trinity_run_de_analysis/2.8.4 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/trinity_samples_qccheck/trinity_samples_qccheck/2.8.4 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/trinotate/trinotate/3.1.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.32.3 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
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