GTN_differential_isoform_expression

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Collection\nRNA-seq data collection"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nGenome annotation"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nReference genome"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nPfam-A HMM library"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Dataset\nPfam-A HMM Stockholm file"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["ℹ️ Input Dataset\nActive sites dataset"];
  style 5 stroke:#2c3143,stroke-width:4px;
  6["ℹ️ Input Dataset\nCPAT header"];
  style 6 stroke:#2c3143,stroke-width:4px;
  7["Flatten collection"];
  0 -->|output| 7;
  8["fastp"];
  0 -->|output| 8;
  9["Convert GTF to BED12"];
  1 -->|output| 9;
  10["Search in textfiles"];
  1 -->|output| 10;
  11["Search in textfiles"];
  1 -->|output| 11;
  12["FastQC"];
  7 -->|output| 12;
  13["gather fastp reports"];
  8 -->|report_json| 13;
  14["RNA STAR"];
  1 -->|output| 14;
  2 -->|output| 14;
  8 -->|output_paired_coll| 14;
  15["Gene BED To Exon/Intron/Codon BED"];
  9 -->|bed_file| 15;
  16["gffread"];
  10 -->|output| 16;
  2 -->|output| 16;
  17["gffread"];
  11 -->|output| 17;
  2 -->|output| 17;
  18["gather FastQC reports"];
  12 -->|text_file| 18;
  19["Concatenate datasets"];
  14 -->|splice_junctions| 19;
  20["Compute"];
  15 -->|out_file1| 20;
  21["Filter"];
  19 -->|out_file1| 21;
  22["Sort"];
  20 -->|out_file1| 22;
  23["Cut"];
  21 -->|out_file1| 23;
  24["Text reformatting"];
  22 -->|out_file1| 24;
  25["Text reformatting"];
  22 -->|out_file1| 25;
  26["Sort"];
  23 -->|out_file1| 26;
  27["Unique lines"];
  26 -->|out_file1| 27;
  28["RNA STAR"];
  1 -->|output| 28;
  2 -->|output| 28;
  8 -->|output_paired_coll| 28;
  27 -->|outfile| 28;
  29["StringTie"];
  1 -->|output| 29;
  28 -->|mapped_reads| 29;
  30["Infer Experiment"];
  28 -->|mapped_reads| 30;
  9 -->|bed_file| 30;
  31["Gene Body Coverage BAM"];
  28 -->|mapped_reads| 31;
  9 -->|bed_file| 31;
  32["Junction Saturation"];
  28 -->|mapped_reads| 32;
  9 -->|bed_file| 32;
  33["Junction Annotation"];
  28 -->|mapped_reads| 33;
  9 -->|bed_file| 33;
  34["Inner Distance"];
  28 -->|mapped_reads| 34;
  9 -->|bed_file| 34;
  35["Read Distribution"];
  28 -->|mapped_reads| 35;
  9 -->|bed_file| 35;
  36["StringTie merge"];
  1 -->|output| 36;
  29 -->|output_gtf| 36;
  37["gffread"];
  29 -->|output_gtf| 37;
  2 -->|output| 37;
  38["MultiQC"];
  28 -->|output_log| 38;
  28 -->|reads_per_gene| 38;
  30 -->|output| 38;
  32 -->|outputr| 38;
  31 -->|outputtxt| 38;
  34 -->|outputfreqtxt| 38;
  35 -->|output| 38;
  33 -->|stats| 38;
  39["StringTie"];
  36 -->|out_gtf| 39;
  28 -->|mapped_reads| 39;
  40["GffCompare"];
  1 -->|output| 40;
  36 -->|out_gtf| 40;
  41["Plot a transcript in intron"];
  28 -->|signal_unique_str2| 41;
  28 -->|signal_unique_str1| 41;
  36 -->|out_gtf| 41;
  42["gffread"];
  36 -->|out_gtf| 42;
  2 -->|output| 42;
  43["Plot ADD3"];
  28 -->|signal_unique_str2| 43;
  28 -->|signal_unique_str1| 43;
  36 -->|out_gtf| 43;
  44["Plot ADD3 zoomed"];
  28 -->|signal_unique_str2| 44;
  28 -->|signal_unique_str1| 44;
  36 -->|out_gtf| 44;
  45["rnaQUAST"];
  1 -->|output| 45;
  2 -->|output| 45;
  37 -->|output_exons| 45;
  46["Extract element identifiers"];
  39 -->|transcript_expression| 46;
  47["Filter"];
  40 -->|tmap_output| 47;
  48["Search in textfiles"];
  46 -->|output| 48;
  49["Filter collection"];
  48 -->|output| 49;
  39 -->|transcript_expression| 49;
  50["IsoformSwitchAnalyzeR"];
  1 -->|output| 50;
  49 -->|output_discarded| 50;
  36 -->|out_gtf| 50;
  49 -->|output_filtered| 50;
  42 -->|output_exons| 50;
  51["IsoformSwitchAnalyzeR"];
  50 -->|switchList| 51;
  52["PfamScan"];
  5 -->|output| 52;
  51 -->|isoformAA| 52;
  4 -->|output| 52;
  3 -->|output| 52;
  53["CPAT"];
  16 -->|output_exons| 53;
  51 -->|isoformNT| 53;
  17 -->|output_exons| 53;
  2 -->|output| 53;
  54["Cut"];
  53 -->|orf_seqs_prob_best| 54;
  55["Add column"];
  54 -->|out_file1| 55;
  56["Remove beginning"];
  55 -->|out_file1| 56;
  57["Concatenate datasets"];
  6 -->|output| 57;
  56 -->|out_file1| 57;
  58["IsoformSwitchAnalyzeR"];
  57 -->|out_file1| 58;
  52 -->|output| 58;
  51 -->|switchList| 58;
  59["IsoformSwitchAnalyzeR"];
  57 -->|out_file1| 59;
  52 -->|output| 59;
  51 -->|switchList| 59;
  d2f0865b-20ba-43ef-8ebc-ad9f517ec60d["Output\nconsequencesSummary"];
  59 --> d2f0865b-20ba-43ef-8ebc-ad9f517ec60d;
  style d2f0865b-20ba-43ef-8ebc-ad9f517ec60d stroke:#2c3143,stroke-width:4px;
  8dd90968-6ef6-48e1-a104-547cbeaa80c8["Output\nconsequencesEnrichment"];
  59 --> 8dd90968-6ef6-48e1-a104-547cbeaa80c8;
  style 8dd90968-6ef6-48e1-a104-547cbeaa80c8 stroke:#2c3143,stroke-width:4px;
  6b812e8d-997d-4a53-9c4f-cb2aa3bb26bc["Output\nsplicingEnrichment"];
  59 --> 6b812e8d-997d-4a53-9c4f-cb2aa3bb26bc;
  style 6b812e8d-997d-4a53-9c4f-cb2aa3bb26bc stroke:#2c3143,stroke-width:4px;
  9c8369e2-8f86-4984-a47a-a35415ecb9b9["Output\nmostSwitching"];
  59 --> 9c8369e2-8f86-4984-a47a-a35415ecb9b9;
  style 9c8369e2-8f86-4984-a47a-a35415ecb9b9 stroke:#2c3143,stroke-width:4px;
  292b9609-061f-49f7-94fc-7831526bb48b["Output\nsplicingSummary"];
  59 --> 292b9609-061f-49f7-94fc-7831526bb48b;
  style 292b9609-061f-49f7-94fc-7831526bb48b stroke:#2c3143,stroke-width:4px;

Inputs

Outputs

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

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/differential-isoform-expression/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