Metatranscriptomics analysis using microbiome RNA-seq data

Run Workflow in Galaxy

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• Import to another server (≥23.0+ only!)

flowchart TD
  0["ℹ️ Input Dataset\nReverse raw reads"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nForward raw reads"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["FastQC"];
  0 -->|output| 2;
  676cd11f-0479-47c4-a23b-c6c8ed5a7790["Output\nfastqc_reverse_html_file"];
  2 --> 676cd11f-0479-47c4-a23b-c6c8ed5a7790;
  style 676cd11f-0479-47c4-a23b-c6c8ed5a7790 stroke:#2c3143,stroke-width:4px;
  3["FastQC"];
  1 -->|output| 3;
  1fb52b78-c905-43c7-a295-d628c996d35a["Output\nfastqc_forward_html_file"];
  3 --> 1fb52b78-c905-43c7-a295-d628c996d35a;
  style 1fb52b78-c905-43c7-a295-d628c996d35a stroke:#2c3143,stroke-width:4px;
  4["Cutadapt"];
  1 -->|output| 4;
  0 -->|output| 4;
  0e7406ed-9eca-486e-b19a-4cbbf04b5138["Output\ncutadapt_report"];
  4 --> 0e7406ed-9eca-486e-b19a-4cbbf04b5138;
  style 0e7406ed-9eca-486e-b19a-4cbbf04b5138 stroke:#2c3143,stroke-width:4px;
  5["MultiQC"];
  2 -->|text_file| 5;
  3 -->|text_file| 5;
  d9f371dd-aa6c-4540-b62b-0e34c0b71afa["Output\nmultiqc_html_report"];
  5 --> d9f371dd-aa6c-4540-b62b-0e34c0b71afa;
  style d9f371dd-aa6c-4540-b62b-0e34c0b71afa stroke:#2c3143,stroke-width:4px;
  6["Filter with SortMeRNA"];
  4 -->|out1| 6;
  4 -->|out2| 6;
  3092eb62-d7fc-4d66-bf57-4c6cf491d0e3["Output\nsortmerna_unaligned_reverse"];
  6 --> 3092eb62-d7fc-4d66-bf57-4c6cf491d0e3;
  style 3092eb62-d7fc-4d66-bf57-4c6cf491d0e3 stroke:#2c3143,stroke-width:4px;
  db3bb8ee-8af7-4528-be4b-f3ea6d381856["Output\nsortmerna_unaligned_forward"];
  6 --> db3bb8ee-8af7-4528-be4b-f3ea6d381856;
  style db3bb8ee-8af7-4528-be4b-f3ea6d381856 stroke:#2c3143,stroke-width:4px;
  7["FASTQ interlacer"];
  6 -->|unaligned_forward| 7;
  6 -->|unaligned_reverse| 7;
  8["MetaPhlAn"];
  6 -->|unaligned_forward| 8;
  6 -->|unaligned_reverse| 8;
  b13521db-f5e7-4bf3-b7fa-673d13fc2911["Output\nmetaphlan_predicted_taxons"];
  8 --> b13521db-f5e7-4bf3-b7fa-673d13fc2911;
  style b13521db-f5e7-4bf3-b7fa-673d13fc2911 stroke:#2c3143,stroke-width:4px;
  9["Cut"];
  8 -->|output_file| 9;
  10["Krona pie chart"];
  8 -->|krona_output_file| 10;
  11["HUMAnN"];
  7 -->|outfile_pairs| 11;
  8 -->|output_file| 11;
  5aec39b6-317a-4fd0-b906-22d5a965e957["Output\nhumann_pathabundance"];
  11 --> 5aec39b6-317a-4fd0-b906-22d5a965e957;
  style 5aec39b6-317a-4fd0-b906-22d5a965e957 stroke:#2c3143,stroke-width:4px;
  53259a06-0783-4db8-828e-328e7337f5b3["Output\nhumann_gene_families"];
  11 --> 53259a06-0783-4db8-828e-328e7337f5b3;
  style 53259a06-0783-4db8-828e-328e7337f5b3 stroke:#2c3143,stroke-width:4px;
  12["Export to GraPhlAn"];
  9 -->|out_file1| 12;
  13["Split a HUMAnN table"];
  11 -->|gene_families_tsv| 13;
  14["Regroup"];
  11 -->|gene_families_tsv| 14;
  15["Renormalize"];
  11 -->|gene_families_tsv| 15;
  4bd1c47e-66ac-41ff-bce9-51d0d86d2252["Output\nrenormalize_gene_families"];
  15 --> 4bd1c47e-66ac-41ff-bce9-51d0d86d2252;
  style 4bd1c47e-66ac-41ff-bce9-51d0d86d2252 stroke:#2c3143,stroke-width:4px;
  16["Rename features"];
  11 -->|gene_families_tsv| 16;
  17["Renormalize"];
  11 -->|pathabundance_tsv| 17;
  1715a5f6-3ac3-4ad2-a030-9307721e2b49["Output\nrenormalize_pathabundance"];
  17 --> 1715a5f6-3ac3-4ad2-a030-9307721e2b49;
  style 1715a5f6-3ac3-4ad2-a030-9307721e2b49 stroke:#2c3143,stroke-width:4px;
  18["Split a HUMAnN table"];
  11 -->|pathabundance_tsv| 18;
  19["Generation, personalization and annotation of tree"];
  12 -->|annotation| 19;
  12 -->|tree| 19;
  20["Split a HUMAnN table"];
  14 -->|output| 20;
  21["Rename features"];
  14 -->|output| 21;
  22["Replace"];
  15 -->|output| 22;
  23["Unpack pathway abundances"];
  15 -->|output| 23;
  17 -->|output| 23;
  b24357e8-b6d3-4893-af63-ac4cf7494b33["Output\nunpack_pathway_abundance"];
  23 --> b24357e8-b6d3-4893-af63-ac4cf7494b33;
  style b24357e8-b6d3-4893-af63-ac4cf7494b33 stroke:#2c3143,stroke-width:4px;
  24["GraPhlAn"];
  19 -->|output_tree| 24;
  21fca66f-dce0-496f-994f-dc8e855e0c8f["Output\ngraphlan_output_image"];
  24 --> 21fca66f-dce0-496f-994f-dc8e855e0c8f;
  style 21fca66f-dce0-496f-994f-dc8e855e0c8f stroke:#2c3143,stroke-width:4px;
  25["Select"];
  21 -->|output| 25;
  946a04fd-1854-4f08-8df1-1a3165651bae["Output\ncc_go"];
  25 --> 946a04fd-1854-4f08-8df1-1a3165651bae;
  style 946a04fd-1854-4f08-8df1-1a3165651bae stroke:#2c3143,stroke-width:4px;
  26["Select"];
  21 -->|output| 26;
  4f5f0597-39eb-42ce-8dd8-d920b52231c3["Output\nbp_go"];
  26 --> 4f5f0597-39eb-42ce-8dd8-d920b52231c3;
  style 4f5f0597-39eb-42ce-8dd8-d920b52231c3 stroke:#2c3143,stroke-width:4px;
  27["Select"];
  21 -->|output| 27;
  28["Combine MetaPhlAn and HUMAnN outputs"];
  22 -->|outfile| 28;
  8 -->|output_file| 28;
  4730e437-6259-44d8-8374-60d6a737b720["Output\ncombined_metaphlan_humann"];
  28 --> 4730e437-6259-44d8-8374-60d6a737b720;
  style 4730e437-6259-44d8-8374-60d6a737b720 stroke:#2c3143,stroke-width:4px;
  29["Split a HUMAnN table"];
  25 -->|out_file1| 29;
  30["Split a HUMAnN table"];
  26 -->|out_file1| 30;
  31["Sort"];
  27 -->|out_file1| 31;
  71abb759-b51f-4383-a791-27d8b1325e81["Output\nsorted_mf_go"];
  31 --> 71abb759-b51f-4383-a791-27d8b1325e81;
  style 71abb759-b51f-4383-a791-27d8b1325e81 stroke:#2c3143,stroke-width:4px;
  32["Split a HUMAnN table"];
  27 -->|out_file1| 32;
  33["Group"];
  28 -->|gene_families_output_file| 33;
  34["Group"];
  28 -->|gene_families_output_file| 34;

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

1. Click on galaxy-workflows-activity Workflows in the Galaxy activity bar (on the left side of the screen, or in the top menu bar of older Galaxy instances). You will see a list of all your workflows
2. Click on galaxy-upload Import at the top-right of the screen
3. 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”
4. 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/microbiome/tutorials/metatranscriptomics/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