De novo transcriptome reconstruction with RNA-Seq

Run Workflow in Galaxy

• Galaxy France
• Galaxy Australia
• Galaxy Main
• Galaxy Europe
• Import to another server (≥23.0+ only!)

flowchart TD
  0["ℹ️ Input Dataset\nG1E_rep1_forward_read"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nG1E_rep1_reverse_read"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nG1E_rep2_forward_read"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nG1E_rep2_reverse_read"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Dataset\nMegakaryocyte_rep1_forward_read"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["ℹ️ Input Dataset\nMegakaryocyte_rep1_reverse_read"];
  style 5 stroke:#2c3143,stroke-width:4px;
  6["ℹ️ Input Dataset\nMegakaryocyte_rep2_forward_read"];
  style 6 stroke:#2c3143,stroke-width:4px;
  7["ℹ️ Input Dataset\nMegakaryocyte_rep2_reverse_read"];
  style 7 stroke:#2c3143,stroke-width:4px;
  8["ℹ️ Input Dataset\nRefSeq_reference_GTF"];
  style 8 stroke:#2c3143,stroke-width:4px;
  9["FastQC"];
  0 -->|output| 9;
  10["FastQC"];
  1 -->|output| 10;
  11["Trimmomatic"];
  0 -->|output| 11;
  1 -->|output| 11;
  12["FastQC"];
  2 -->|output| 12;
  13["FastQC"];
  3 -->|output| 13;
  14["Trimmomatic"];
  2 -->|output| 14;
  3 -->|output| 14;
  15["FastQC"];
  4 -->|output| 15;
  16["FastQC"];
  5 -->|output| 16;
  17["Trimmomatic"];
  4 -->|output| 17;
  5 -->|output| 17;
  18["FastQC"];
  6 -->|output| 18;
  19["FastQC"];
  7 -->|output| 19;
  20["Trimmomatic"];
  6 -->|output| 20;
  7 -->|output| 20;
  21["HISAT2"];
  11 -->|fastq_out_r1_paired| 21;
  11 -->|fastq_out_r2_paired| 21;
  22["FastQC"];
  11 -->|fastq_out_r1_paired| 22;
  23["FastQC"];
  11 -->|fastq_out_r2_paired| 23;
  24["HISAT2"];
  14 -->|fastq_out_r1_paired| 24;
  14 -->|fastq_out_r2_paired| 24;
  25["FastQC"];
  14 -->|fastq_out_r1_paired| 25;
  26["FastQC"];
  14 -->|fastq_out_r2_paired| 26;
  27["HISAT2"];
  17 -->|fastq_out_r1_paired| 27;
  17 -->|fastq_out_r2_paired| 27;
  28["FastQC"];
  17 -->|fastq_out_r1_paired| 28;
  29["FastQC"];
  17 -->|fastq_out_r2_paired| 29;
  30["HISAT2"];
  20 -->|fastq_out_r1_paired| 30;
  20 -->|fastq_out_r2_paired| 30;
  31["FastQC"];
  20 -->|fastq_out_r1_paired| 31;
  32["FastQC"];
  20 -->|fastq_out_r2_paired| 32;
  33["StringTie"];
  21 -->|output_alignments| 33;
  34["bamCoverage"];
  21 -->|output_alignments| 34;
  35["bamCoverage"];
  21 -->|output_alignments| 35;
  36["StringTie"];
  24 -->|output_alignments| 36;
  37["bamCoverage"];
  24 -->|output_alignments| 37;
  38["bamCoverage"];
  24 -->|output_alignments| 38;
  39["StringTie"];
  27 -->|output_alignments| 39;
  40["bamCoverage"];
  27 -->|output_alignments| 40;
  41["bamCoverage"];
  27 -->|output_alignments| 41;
  42["StringTie"];
  30 -->|output_alignments| 42;
  43["bamCoverage"];
  30 -->|output_alignments| 43;
  44["bamCoverage"];
  30 -->|output_alignments| 44;
  45["StringTie merge"];
  8 -->|output| 45;
  33 -->|output_gtf| 45;
  36 -->|output_gtf| 45;
  42 -->|output_gtf| 45;
  39 -->|output_gtf| 45;
  46["GffCompare"];
  8 -->|output| 46;
  45 -->|out_gtf| 46;
  47["featureCounts"];
  21 -->|output_alignments| 47;
  46 -->|transcripts_annotated| 47;
  48["featureCounts"];
  24 -->|output_alignments| 48;
  46 -->|transcripts_annotated| 48;
  49["featureCounts"];
  27 -->|output_alignments| 49;
  46 -->|transcripts_annotated| 49;
  50["featureCounts"];
  30 -->|output_alignments| 50;
  46 -->|transcripts_annotated| 50;
  51["DESeq2"];
  47 -->|output_short| 51;
  48 -->|output_short| 51;
  49 -->|output_short| 51;
  50 -->|output_short| 51;
  52["Filter"];
  51 -->|deseq_out| 52;
  53["Filter"];
  52 -->|out_file1| 53;
  54["Filter"];
  52 -->|out_file1| 54;

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

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:

Version History

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/de-novo/workflows/transcriptomics-denovo-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