Workflows

These workflows are associated with Whole transcriptome analysis of Arabidopsis thaliana

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.

Plant bulk RNA-Seq workflow

Last updated Jan 20, 2023

Launch in Tutorial Mode question
License: None Specified, defaults to CC-BY-4.0
Tests: ❌ Results: Not yet automated

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;
	

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