Comments (4)
Hi Fabricio,
thanks a lot - that would be great! On my side, I agree with your suggested workflow (my preference though would be to directly use tximeta rather than tximport
as it involves less downstream fiddling to get the object into a suitable shape for further analysis). It would probably also be good to have a short introduction on the biological/technological side - describing what we are actually measuring with RNA-seq.
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Thank you for your feedback, Charlotte.
Indeed, tximeta would be better. I will see what I can do to avoid having to download huge FASTQ files from ENA to use in the episode. I think there might be some nice FASTQ files on ExperimentHub that I can use.
I will also try to write a short intro on what RNA-seq is.
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Thank you for bringing these points up, Jenny.
fastp and salmon can be run on a laptop without problems (I myself have done it on an Ubuntu laptop with 8 GB RAM). The issue here might be compatibility with multiple platforms. I have not tried installing fastp and salmon on Windows and macOS, so I'm not sure if that would be an issue. I will try that asap and let you know.
I saw the discussion on Slack, and I will try to think of solutions to this issue, from using Orchestra to Desktop.
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Related Issues (20)
- Update life cycle stage? HOT 1
- Replace UCSC with NCBI
- Put subheadings in Episode 1
- Should we switch to TidySummarizedExperiment?
- Add > PCs to iSEE example OR add glimmaMDS
- Add authors
- To Do before BioC2023 workshop HOT 3
- Populate "Download Lesson Handout"
- Expand episode 1 to include experimental design & batch effects HOT 2
- Extras to add to episode 4
- suggest episode re-order to 5. DE analysis, 6. Exploration of design matrices, 7. Re-visit practice data analysis, 8. Gene set HOT 1
- Add links to public FastQC reports
- Add intro to GRanges, or create an unranged SE
- Save assembled SE object in output/ rather than in data/
- Change color palette in barplot
- Add iSEE-related challenges
- Add more exercises to gene set analysis episode
- Add workflow diagram
- Mention volcano plots
- Add links to bioc-project
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