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added galaxy exercises #1

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07a08cd
added galaxy exercises
ramobrah Oct 20, 2022
e9beb5e
Added RNAseq galaxy
ramobrah Oct 21, 2022
4137bd0
fixed links
ramobrah Oct 21, 2022
8f750d6
another fix to links
ramobrah Oct 21, 2022
4d92a4a
added subbullets
ramobrah Oct 21, 2022
dc82b30
indented basic exercises
ramobrah Oct 23, 2022
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14 changes: 9 additions & 5 deletions README.md
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Expand Up @@ -32,11 +32,13 @@ Learn how to use online resources for genomic-scale data analysis of protozoan p

Day 1:

- [Basic searches in VEuPathDB – Site search](https://github.com/WCSCourses/Protozoan_Parasite_Database_Resources_2022/blob/main/Manuals/1_SiteSearch_PlasmoDB.pdf)
- Basic searches in VEuPathDB:

- [Basic searches in VEuPathDB – Search strategies](https://github.com/WCSCourses/Protozoan_Parasite_Database_Resources_2022/blob/main/Manuals/1b_SearchStrategies_Exercise_PlasmoDB.pdf)
- [Basic searches in VEuPathDB – Site search](https://github.com/WCSCourses/Protozoan_Parasite_Database_Resources_2022/blob/main/Manuals/1_SiteSearch_PlasmoDB.pdf)

- [Basic searches in VEuPathDB – Organism Preferences (optional exercise)](https://github.com/WCSCourses/Protozoan_Parasite_Database_Resources_2022/blob/main/Manuals/1c_Organism_Preferences.pdf)
- [Basic searches in VEuPathDB – Search strategies](https://github.com/WCSCourses/Protozoan_Parasite_Database_Resources_2022/blob/main/Manuals/1b_SearchStrategies_Exercise_PlasmoDB.pdf)

- [Basic searches in VEuPathDB – Organism Preferences (optional exercise)](https://github.com/WCSCourses/Protozoan_Parasite_Database_Resources_2022/blob/main/Manuals/1c_Organism_Preferences.pdf)

- [The gene page in VEuPathDB](https://github.com/WCSCourses/Protozoan_Parasite_Database_Resources_2022/blob/main/Manuals/2_Exploring_the_Gene_Page.pdf)

Expand All @@ -63,14 +65,16 @@ Learn how to use online resources for genomic-scale data analysis of protozoan p
Day 3:

- Intro to RNA Seq Analysis - will be a talk - slides will come.
- Group exercise: Starting and RNA Seq analysis workflow in Galaxy
- [Groups](https://github.com/WCSCourses/Protozoan_Parasite_Database_Resources_2022/blob/main/Manuals/RNAseq%20groups.pdf)
- [RNA Seq in Galaxy part 1](https://github.com/WCSCourses/Protozoan_Parasite_Database_Resources_2022/blob/main/Manuals/RNAseq_Mapping_Galaxy_part1.pdf)

- [Transcriptomics/proteomic searches in VEuPathDB](https://github.com/WCSCourses/Protozoan_Parasite_Database_Resources_2022/blob/main/Manuals/6b_Proteomics.pdf)

- [Orthology](https://github.com/WCSCourses/Protozoan_Parasite_Database_Resources_2022/blob/main/Manuals/7_Orthology_Phyletic_Patterns.pdf)

Day 4:

- GO enrichment analysis
- [Exploring RNA Seq results from Galaxy part 2, including analysis of results in VEuPathDB](https://github.com/WCSCourses/Protozoan_Parasite_Database_Resources_2022/blob/main/Manuals/RNAseq_Mapping_Galaxy_part2.pdf)

- Host response

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