Warning: Please be aware that these videos are a snapshot, and as such may use an outdated version of the tutorial and/or Galaxy. Below the video you will find links to the tutorials as they appeared at the time of recording.
Below are video tutorials for this GTN session, created for various (past) events.
Proteogenomics is a field of biological research that utilizes a combination of proteomics, genomics, and transcriptomics to aid in the discovery and identification of peptides
Proteogenomics 1: Database Creation (Tutorial)
| Description: | In this tutorial, we will provide a walkthrough on how to generate a customized protein sequence database using RNA-Seq data. The resultant FASTA database contains sequences with single amino acid variants (SAVs), insertions and deletions (indels)and transcript assemblies (splicing variants). This database can then be used to identify protein sequence variants from the mass spectrometry data. |
| Length: | 40 minutes |
| Captions: | Emma Leith |
| Created: | 15 February 2021 |
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| Supported Servers: | Known Working Possibly Working |
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Proteogenomics 2: Database Search (Demo)
| Description: | In this demonstration, we’re continuing the process of proteogenomic analysis. Here, we search mass spectrometry data against a custom proteogenomics FASTA database to create peptide spectral matches (PSMs) for each dataset; we also isolate non-canonical peptides from the resulting data for further analysis. If you would like to view the results yourself, we provide example histories in the FAQ document |
| Length: | 30 minutes |
| Captions: | Emma Leith |
| Created: | 15 February 2021 |
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| Supported Servers: | Known Working Possibly Working |
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Proteogenomics 3: Novel peptide analysis (Demo)
| Description: | In this demonstration, we will investigate the peptides that were identified during proteogenomics tutorial 2. We will identify the presence of novel proteoforms that are absent in the reference database, annotate the novel peptides and visualize them using the Multi-omics Visualization Platform (MVP). If you would like to view the results yourself, we provide example histories in the FAQ document |
| Length: | 40 minutes |
| Captions: | Subina Mehta |
| Created: | 15 February 2021 |
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| Supported Servers: | Known Working Possibly Working |
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