Proteogenomics 1: Database Creation

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\nTrimmed_ref_5000_uniprot_cRAP.fasta"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nFASTQ_ProB_22LIST.fastqsanger"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nReference Annotation"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Parameter\nReference Genome"];
  style 3 fill:#ded,stroke:#393,stroke-width:4px;
  4["ℹ️ Input Parameter\nReference Genome Annotation for CustomProDB"];
  style 4 fill:#ded,stroke:#393,stroke-width:4px;
  5["Filter Tabular"];
  0 -->|output| 5;
  6["Replace Text"];
  2 -->|output| 6;
  da9f13a5-80a6-4ed5-8563-b3135cf2bb07["Output\nReference Annotation fixed.gtf"];
  6 --> da9f13a5-80a6-4ed5-8563-b3135cf2bb07;
  style da9f13a5-80a6-4ed5-8563-b3135cf2bb07 stroke:#2c3143,stroke-width:4px;
  7["HISAT2"];
  1 -->|output| 7;
  3 -->|output| 7;
  8468a5c2-313b-4cc2-8676-3f255c579bdd["Output\nHISAT_Output.BAM"];
  7 --> 8468a5c2-313b-4cc2-8676-3f255c579bdd;
  style 8468a5c2-313b-4cc2-8676-3f255c579bdd stroke:#2c3143,stroke-width:4px;
  8["FreeBayes"];
  7 -->|output_alignments| 8;
  3 -->|output| 8;
  9["StringTie"];
  6 -->|outfile| 9;
  7 -->|output_alignments| 9;
  940b9a6a-19de-4430-8ead-9636f1cfcd4c["Output\nStringtie_output.gtf"];
  9 --> 940b9a6a-19de-4430-8ead-9636f1cfcd4c;
  style 940b9a6a-19de-4430-8ead-9636f1cfcd4c stroke:#2c3143,stroke-width:4px;
  10["CustomProDB"];
  7 -->|output_alignments| 10;
  4 -->|output| 10;
  8 -->|output_vcf| 10;
  11["GffCompare"];
  2 -->|output| 11;
  9 -->|output_gtf| 11;
  171de99f-3ec1-487f-92bc-9919dc0d904a["Output\ntranscripts_annotated"];
  11 --> 171de99f-3ec1-487f-92bc-9919dc0d904a;
  style 171de99f-3ec1-487f-92bc-9919dc0d904a stroke:#2c3143,stroke-width:4px;
  12["FASTA Merge Files and Filter Unique Sequences"];
  10 -->|output_rpkm| 12;
  10 -->|output_snv| 12;
  10 -->|output_indel| 12;
  04a7cf44-f98a-4dca-99e5-9a1ae56dbb0d["Output\nMerged and Filtered FASTA from CustomProDB"];
  12 --> 04a7cf44-f98a-4dca-99e5-9a1ae56dbb0d;
  style 04a7cf44-f98a-4dca-99e5-9a1ae56dbb0d stroke:#2c3143,stroke-width:4px;
  13["SQLite to tabular"];
  10 -->|output_genomic_mapping_sqlite| 13;
  5fb81959-b607-4d81-89b5-9da027c538d1["Output\ngenomic_mapping_sqlite"];
  13 --> 5fb81959-b607-4d81-89b5-9da027c538d1;
  style 5fb81959-b607-4d81-89b5-9da027c538d1 stroke:#2c3143,stroke-width:4px;
  14["SQLite to tabular"];
  10 -->|output_variant_annotation_sqlite| 14;
  a5cc8d8b-3401-46c1-a0d0-eb5af7d04b4c["Output\nvariant_annotation_sqlite"];
  14 --> a5cc8d8b-3401-46c1-a0d0-eb5af7d04b4c;
  style a5cc8d8b-3401-46c1-a0d0-eb5af7d04b4c stroke:#2c3143,stroke-width:4px;
  15["FASTA-to-Tabular"];
  10 -->|output_rpkm| 15;
  16["Convert gffCompare annotated GTF to BED"];
  11 -->|transcripts_annotated| 16;
  17["FASTA-to-Tabular"];
  12 -->|output| 17;
  18["Column Regex Find And Replace"];
  13 -->|query_results| 18;
  1d644076-da23-4303-81c9-63e5e87cb053["Output\nSAV_INDEL"];
  18 --> 1d644076-da23-4303-81c9-63e5e87cb053;
  style 1d644076-da23-4303-81c9-63e5e87cb053 stroke:#2c3143,stroke-width:4px;
  19["Column Regex Find And Replace"];
  14 -->|query_results| 19;
  45749ecf-369c-4569-965a-261dcce60d23["Output\nvariant_annotation"];
  19 --> 45749ecf-369c-4569-965a-261dcce60d23;
  style 45749ecf-369c-4569-965a-261dcce60d23 stroke:#2c3143,stroke-width:4px;
  20["Filter Tabular"];
  15 -->|output| 20;
  21["Translate BED transcripts"];
  16 -->|output| 21;
  3119e0c0-30d4-49dd-bdc9-56ca6d7fbbc2["Output\nTranslate cDNA_minus_CDS"];
  21 --> 3119e0c0-30d4-49dd-bdc9-56ca6d7fbbc2;
  style 3119e0c0-30d4-49dd-bdc9-56ca6d7fbbc2 stroke:#2c3143,stroke-width:4px;
  22["Column Regex Find And Replace"];
  17 -->|output| 22;
  23["Query Tabular"];
  19 -->|out_file1| 23;
  de055cf9-fab7-4848-a518-135e3f895fc6["Output\nVariant_annotation_sqlitedb"];
  23 --> de055cf9-fab7-4848-a518-135e3f895fc6;
  style de055cf9-fab7-4848-a518-135e3f895fc6 stroke:#2c3143,stroke-width:4px;
  24["Concatenate multiple datasets"];
  20 -->|output| 24;
  5 -->|output| 24;
  25["bed to protein map"];
  21 -->|translation_bed| 25;
  26["Tabular-to-FASTA"];
  22 -->|out_file1| 26;
  d57ef383-ba16-42c2-9ee9-4fdb4acca1a2["Output\nCustomProDB Merged Fasta"];
  26 --> d57ef383-ba16-42c2-9ee9-4fdb4acca1a2;
  style d57ef383-ba16-42c2-9ee9-4fdb4acca1a2 stroke:#2c3143,stroke-width:4px;
  27["Concatenate multiple datasets"];
  18 -->|out_file1| 27;
  25 -->|output| 27;
  b30d6097-a709-42d3-933a-aeedc4e90ec6["Output\nGenomic_Protein_map"];
  27 --> b30d6097-a709-42d3-933a-aeedc4e90ec6;
  style b30d6097-a709-42d3-933a-aeedc4e90ec6 stroke:#2c3143,stroke-width:4px;
  28["FASTA Merge Files and Filter Unique Sequences"];
  26 -->|output| 28;
  21 -->|translation_fasta| 28;
  0 -->|output| 28;
  ce87fe82-008d-404d-b512-034116326e1e["Output\nUniprot_cRAP_SAV_indel_translatedbed"];
  28 --> ce87fe82-008d-404d-b512-034116326e1e;
  style ce87fe82-008d-404d-b512-034116326e1e stroke:#2c3143,stroke-width:4px;
  29["Query Tabular"];
  27 -->|out_file1| 29;
  d470b980-5ccc-4217-91fb-ced35304e854["Output\ngenomic_mapping_sqlitedb"];
  29 --> d470b980-5ccc-4217-91fb-ced35304e854;
  style d470b980-5ccc-4217-91fb-ced35304e854 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

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/proteomics/tutorials/proteogenomics-dbcreation/workflows/galaxy-workflow-mouse_rnaseq_dbcreation.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