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Created November 11, 2014 06:27
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Proteogenomics
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ingalaxy.md

Running a Proteogenomics Analysis in Galaxy

To do this properly you need to follow this basic pattern of steps regardless of the project.

  1. Create a protein database that you can also generate a gff coordinate file for.
  2. Run proteomic searches on this db to create a protXML file
  3. Use the Proteomics to GFF tool to map proteomics results back to your genomic coordinates.

Analysing a transcriptome

Step 1: Import your transcriptome (as nucleic acid sequences)

Step 2: Use the Generate 6 frame translation tool to create a protein fasta file from your transcriptome

Step 3: Use the Generate 6 frame translation again but specify the gff output option to generate corresponding gff coordinates

Step 4: Run proteomics searches using the protein fasta file

Step 5: Combine results with the Proteomics to GFF tool

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