Genome-wide alternative splicing analysis: human

Run Workflow in Galaxy

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• 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\nReference genome"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nGenome annotation"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nControl IDs"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Parameter\nFactor 02"];
  style 4 fill:#ded,stroke:#393,stroke-width:4px;
  5["ℹ️ Input Parameter\nFactor 01"];
  style 5 fill:#ded,stroke:#393,stroke-width:4px;
  6["ℹ️ Input Dataset\nCPAT header"];
  style 6 stroke:#2c3143,stroke-width:4px;
  7["ℹ️ Input Dataset\nActive sites dataset"];
  style 7 stroke:#2c3143,stroke-width:4px;
  8["ℹ️ Input Dataset\nPfam-A HMM Stockholm file"];
  style 8 stroke:#2c3143,stroke-width:4px;
  9["ℹ️ Input Dataset\nPfam-A HMM library"];
  style 9 stroke:#2c3143,stroke-width:4px;
  10["fastp"];
  0 -->|output| 10;
  11["Flatten collection"];
  0 -->|output| 11;
  12["Search in textfiles"];
  2 -->|output| 12;
  13["Search in textfiles"];
  2 -->|output| 13;
  14["Convert GTF to BED12"];
  2 -->|output| 14;
  15["FastQC"];
  11 -->|output| 15;
  16["gffread"];
  12 -->|output| 16;
  1 -->|output| 16;
  e34fd125-e860-48a2-9e58-bed5c3600b8d["Output\nlncRNA sequences"];
  16 --> e34fd125-e860-48a2-9e58-bed5c3600b8d;
  style e34fd125-e860-48a2-9e58-bed5c3600b8d stroke:#2c3143,stroke-width:4px;
  17["gffread"];
  13 -->|output| 17;
  1 -->|output| 17;
  836eeb38-dc67-42df-93fa-2fcd5bbe7a80["Output\nprotein coding sequences"];
  17 --> 836eeb38-dc67-42df-93fa-2fcd5bbe7a80;
  style 836eeb38-dc67-42df-93fa-2fcd5bbe7a80 stroke:#2c3143,stroke-width:4px;
  18["MultiQC"];
  15 -->|text_file| 18;
  10 -->|report_json| 18;
  19["Search in textfiles"];
  15 -->|text_file| 19;
  20["Concatenate datasets"];
  19 -->|output| 20;
  21["Search in textfiles"];
  20 -->|out_file1| 21;
  22["Cut"];
  21 -->|output| 22;
  23["Text reformatting"];
  22 -->|out_file1| 23;
  24["Parse parameter value"];
  23 -->|outfile| 24;
  25["RNA STAR"];
  2 -->|output| 25;
  24 -->|integer_param| 25;
  1 -->|output| 25;
  10 -->|output_paired_coll| 25;
  26["Concatenate datasets"];
  25 -->|splice_junctions| 26;
  27["Text reformatting"];
  26 -->|out_file1| 27;
  28["Cut"];
  27 -->|outfile| 28;
  29["Sort"];
  28 -->|out_file1| 29;
  30["Unique"];
  29 -->|out_file1| 30;
  31["RNA STAR"];
  2 -->|output| 31;
  24 -->|integer_param| 31;
  1 -->|output| 31;
  10 -->|output_paired_coll| 31;
  30 -->|outfile| 31;
  32["StringTie"];
  2 -->|output| 32;
  31 -->|mapped_reads| 32;
  33["Junction Annotation"];
  31 -->|mapped_reads| 33;
  14 -->|bed_file| 33;
  34["Junction Saturation"];
  31 -->|mapped_reads| 34;
  14 -->|bed_file| 34;
  35["Gene Body Coverage BAM"];
  31 -->|mapped_reads| 35;
  14 -->|bed_file| 35;
  36["Inner Distance"];
  31 -->|mapped_reads| 36;
  14 -->|bed_file| 36;
  37["Infer Experiment"];
  31 -->|mapped_reads| 37;
  14 -->|bed_file| 37;
  38["Read Distribution"];
  31 -->|mapped_reads| 38;
  14 -->|bed_file| 38;
  39["gffread"];
  32 -->|output_gtf| 39;
  1 -->|output| 39;
  40["StringTie merge"];
  2 -->|output| 40;
  32 -->|output_gtf| 40;
  41["MultiQC"];
  31 -->|output_log| 41;
  37 -->|output| 41;
  38 -->|output| 41;
  34 -->|outputr| 41;
  33 -->|stats| 41;
  35 -->|outputtxt| 41;
  36 -->|outputfreqtxt| 41;
  42["rnaQUAST"];
  2 -->|output| 42;
  1 -->|output| 42;
  39 -->|output_exons| 42;
  43["gffread"];
  40 -->|out_gtf| 43;
  1 -->|output| 43;
  44["StringTie"];
  40 -->|out_gtf| 44;
  31 -->|mapped_reads| 44;
  45["Filter collection"];
  3 -->|output| 45;
  44 -->|transcript_expression| 45;
  46["IsoformSwitchAnalyzeR"];
  2 -->|output| 46;
  24 -->|integer_param| 46;
  5 -->|output| 46;
  45 -->|output_filtered| 46;
  40 -->|out_gtf| 46;
  4 -->|output| 46;
  45 -->|output_discarded| 46;
  43 -->|output_exons| 46;
  47["IsoformSwitchAnalyzeR"];
  46 -->|switchList| 47;
  48["CPAT"];
  17 -->|output_exons| 48;
  47 -->|isoformNT| 48;
  16 -->|output_exons| 48;
  1 -->|output| 48;
  49["PfamScan"];
  7 -->|output| 49;
  47 -->|isoformAA| 49;
  8 -->|output| 49;
  9 -->|output| 49;
  50["Remove beginning"];
  48 -->|orf_seqs_prob_best| 50;
  51["Text reformatting"];
  50 -->|out_file1| 51;
  52["Concatenate datasets"];
  6 -->|output| 52;
  51 -->|outfile| 52;
  53["IsoformSwitchAnalyzeR"];
  52 -->|out_file1| 53;
  49 -->|output| 53;
  47 -->|switchList| 53;
  54["IsoformSwitchAnalyzeR"];
  52 -->|out_file1| 54;
  49 -->|output| 54;
  47 -->|switchList| 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/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