# ANGUS 2018 - LIONS
[ANGUS Lesson Schedule](https://angus.readthedocs.io/en/2018/) (Gladys Valley Hall, UC Davis, USA)
[These](https://github.com/ngs-docs/angus/blob/2018/online-tools.md) are all the ways we're communicating at [DIBSI 2018](http://ivory.idyll.org/dibsi/toc.html).
Will we find the threshold for communication overload? Stay tuned.
-Using [HackMD](https://hackmd.io/s/features) and [GitHub](https://guides.github.com/activities/hello-world/)
-Unix [cheat sheet](https://hackmd.io/X8_egsBqT52sSZCFPo2cAg), [explanation of commmands](www.explainshell.com), and [additional notes](https://hackmd.io/X8_egsBqT52sSZCFPo2cAg)
-RStudio [cheat sheet](https://www.datacamp.com/community/tutorials/functions-in-r-a-tutorial) and [data viz 101](https://www.rstudio.com/resources/cheatsheets/), as well as [RMarkdown](https://rmarkdown.rstudio.com/articles_intro.html)
-Transcriptome assembly [overview](https://github.com/ngs-docs/angus/blob/2018/compare_transcriptome_assembly_to_ref.md)
## Reference ANGUS [Table of Contents](http://angus.readthedocs.io/en/2018/toc.html)
### Week 1
- [x] [Day 1 [01:30 PM - 05:30 PM]](https://hackmd.io/rA4tpZK8QW6Zk1RFvzdbrg?view): Monday, July 2nd
**(3)** Cloud computers (Jetstream)
**(4)** Using Slack and HackMD
**(5)** Intro to command line for BLAST analyses
**(6)** Intro to R for BLAST analyses and data viz
- [x] [Day 2 [09:00 AM - 05:30 PM]](https://hackmd.io/HI06fzFRSCK4TdhnRClJNw?view): Tuesday, July 3rd
**(5) - (6)** Recap of command line and R for via BLAST
**(7)** Trimming quality control of reads
Tutorial on Twitter as a tool
- [x] [Day 3 [09:00 AM - 12:00 PM]](https://hackmd.io/pFxo86-gQb6tM-WC0LrdZw?view): Wednesday, July 4th
**(7)** Recap of trimmomatic
**(8)** Intro to transcriptome mapping and variant calling
- [x] [Day 4 [09:00 AM - 05:30 PM]](https://hackmd.io/9tFqoUNISo6NJTfeYwk8Pw): Thursday, July 5th
**(8)** Recap of mapping (visualization)
**(9)** Introduction to RNASeq analyses and visualization
More on RStudio and data visualization
- [x] [Day 5 [9:00 AM - 5:30 PM]](https://hackmd.io/Ig4fxhG4RoydP2tq844EhQ): Friday, July 6th
**(9)** Recap of RNA analyses and visualization
**(10)** Transcriptome assembly (basics)
**(11)** On your own: Genome assembly [challenge exercise](http://angus.readthedocs.io/en/2018/genome-assembly.html)
### Weekend (optional)
- [R workshop](https://hackmd.io/P4QKo3J2QvWugtf8IGuqJA?both) and [DESeq2](https://angus.readthedocs.io/en/2017/deseq2-asthma.html#install-the-deseq2-prereqs) [Saturday]
- [UNIX workshop](https://hackmd.io/v6qFLqprSHyRktq42wbfIQ?view) [Saturday]
### Week 2
- [x] [Day 6 [9:00 AM - 5:30 PM]](https://hackmd.io/s/HkCwqMZ77): Monday, July 9th
**(11)** Recap of -omics (Titus Brown)
**(12)** Introduction to bioconda and application
**(13)** Introduction to R markdown, GitHub and Binder via RNAseq
- [x] [Day 7 [9:00 AM - 9:00 PM]](https://hackmd.io/s/BJK4vvfmX): Tuesday, July 10th
**(14)** ChIP-seq tutorial
- [x] [Day 8 [9:00 AM - 4:00 PM]](https://hackmd.io/s/BJFjGpXmX): Wednesday, July 11th
**(15)** Transcriptome annotation
- [x] [Day 9 [9:00 - 5:30 PM]](https://hackmd.io/qkyfi-fiSE-PL_UowSAcDQ): Thursday, July 12th
**(?)** Genome assembly
**(16-21)** Where to put data for publication
- [x] [Day 10 [9:00 - 5:30 PM]](https://hackmd.io/s/Bk0I8PI77): Friday, July 13th
- [x] Day 11 [9:00 AM - 12:00 PM]: Saturday, July 14th
- Not enough time on complex lessons (trimming, mapping, variant calling had all 2 sessions and can be done in one) -leave more time for complex activities and/or breakout groups.
- We need to build some assesment as an activity instead of a form.
- More practice/exercises on alternative datasets.
- Make them draw the workflow diagram.
- We need more workflows, visuals.
- Tutorials where we define all the flags.
- Week 2: leave more open stuff to gather interest.
- Have all the potential lessons ahead of time and have the ability of linking them to the schedule when we need them.
- Have basics of Unix and R at the very beginning of the week- or give them the materials ahead of time. Bring people up to speed.
- Facilitate instructors and helpers to communicate ahead of time. Helpers and instructors meet 1 day ahead of time?
- Organise HackMD? TOC? Centralised somehow.
- Most things worked
- We covered lots of material
- We may feel it worse than it is because of being autocritical
- HackMD notes worked but we need to set their purpose
- Group is happy! We have wine
- Having more helpers is better than less
- Feedback really helps
- Having different people with different languages
- Maybe distribute the teaching load a bit more