New tutorial about genome annotation, comparative genomics and visualization #6481
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topics/genome-annotation/tutorials/genome-annotation-comparison-visualization/tutorial.md
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rlibouba
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rlibouba
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Hello, thank you for this tutorial. Great work!
I've done a first read-through and made some suggestions that you can take into account or not.
The tests fail on lint due to the absence of tests for workflows. A .yml file should be added (example: https://github.com/galaxyproject/training-material/blob/main/topics/genome-annotation/tutorials/helixer/workflows/Helixer-tests.yml). You can generate the skeleton of this file locally. You can find explanations right here: https://github.com/galaxyproject/iwc/tree/main/workflows
| - **Enzyme codes (EC numbers)** | ||
| - **Orthology relationships** | ||
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| > <details-title>Background: Why orthology improves functional annotation</details-title> |
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| > <details-title>Background: Why orthology improves functional annotation</details-title> | |
| > <details-title>Background: Why orthology improves functional annotation?</details-title> |
| - **GO terms** | ||
| - **KEGG pathways** | ||
| - **COG categories** | ||
| - **Enzyme codes (EC numbers)** | ||
| - **Orthology relationships** |
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Perhaps briefly define these terms? Or explain what they are used for?
| {: .hands_on} | ||
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| # Statistics of our genome (gfastats) |
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| # Statistics of our genome (gfastats) | |
| # Statistics of our genome |
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| {: .question} | ||
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| # Preparing RNASeq data (RNA STAR) |
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| # Preparing RNASeq data (RNA STAR) | |
| # Preparing RNASeq data |
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| {: .question} | ||
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| # Functional annotation (EggNOG Mapper, InterProScan and Funannotate functional) |
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| # Functional annotation (EggNOG Mapper, InterProScan and Funannotate functional) | |
| # Functional annotation |
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| Funannotate functional integrates: |
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I think one or two sentences are missing to introduce funannotate functional.
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| {: .question} | ||
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| # Visualisation with a genome browser (JBrowse2) |
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| # Visualisation with a genome browser (JBrowse2) | |
| # Visualisation with a genome browser |
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| This visual inspection is crucial to validating genome annotation results. | ||
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| > <details-title>Background: Why visualization is important</details-title> |
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| > <details-title>Background: Why visualization is important</details-title> | |
| > <details-title>Background: Why visualization is important?</details-title> |
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| # Introduction |
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According to the lint errors, this line must be deleted.
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| { | |||
| "a_galaxy_workflow": "true", | |||
| "annotation": "In this tutorial, you will perform a complete workflow for fungal genome annotation, comparative genomics, and visualization. Starting from raw Mucor mucedo genomic and RNA-seq data, you will run Funannotate to generate structural and functional annotations. The predicted proteome is then compared with complete proteomes from related Mucor species and Saccharomyces cerevisiae using OrthoFinder to identify orthogroups and assess evolutionary relationships. Finally, the annotated genome and comparative results are explored and visualized using JBrowse2 for interactive genome browsing and Circos to display synteny and genomic relationships.", | |||
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Can you summarize it in one or two lines?
shiltemann
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shiltemann
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Thanks a lot @soniacasillas! Just a few very minor comments below. You can simply hit the "Commit Suggestion" button if you agree, to make the change.
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| # Introduction |
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| # Introduction |
We prefer not to start a tutorial with a heading, it makes previews on e.g. chat and social media nicer.
| title: Genome annotation (Funannotate), comparison (OrthoFinder) and visualization | ||
| (JBrowse2 & Circos) [Galaxy Training Material] |
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| title: Genome annotation (Funannotate), comparison (OrthoFinder) and visualization | |
| (JBrowse2 & Circos) [Galaxy Training Material] | |
| title: Genome annotation, comparison and visualization |
I would simplify the title a bit.
(If you really want to keep the tool names you can, but at least remove the "[Galaxy Training Material]" part)
| layout: tutorial_hands_on | ||
| title: Genome annotation (Funannotate), comparison (OrthoFinder) and visualization | ||
| (JBrowse2 & Circos) [Galaxy Training Material] | ||
| zenodo_link: https://zenodo.org/records/17612216 |
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I get a page not found here, could you double-check if this link is correct and public?
| (JBrowse2 & Circos) [Galaxy Training Material] | ||
| zenodo_link: https://zenodo.org/records/17612216 | ||
| tags: | ||
| - genome annotation |
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since it is already in the genome annotation topic, we don't need it as a tag
| - genome annotation |
| > 2. Upload the datasets from **<{{ page.zenodo_link }}>** using either: | ||
| > - **Paste/Fetch data** (URLs from Zenodo), or | ||
| > - **Upload from your computer** after downloading the files. |
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It is easier for users if we provide the direct URLs to all files in a text box that they can easily copy-paste to Galaxy:
| > 2. Upload the datasets from **<{{ page.zenodo_link }}>** using either: | |
| > - **Paste/Fetch data** (URLs from Zenodo), or | |
| > - **Upload from your computer** after downloading the files. | |
| > 2. Click **Paste/Fetch data** and paste in the following URLs in the box that appears. | |
| > | |
| > ``` | |
| > https://zenodo.org/record/17612216/files/link-to-file-1.txt | |
| > https://zenodo.org/record/17612216/files/file2.fasta | |
| > ```` |
3 participants
I added a new tutorial about genome annotation, comparative genomics and visualization (under the topic genome-annotation).
It uses this workflow on UseGalaxy.eu:
https://usegalaxy.eu/u/scasillas/w/genome-annotation-funannotate-comparison-orthofinder-and-visualization-jbrowse2--circos-galaxy-training-material
It is my first contributed tutorial. Please let me know if anything needs to be corrected.
Thank you!