comments from review of day 1 and day 2 material

[ctb]

For https://angus.readthedocs.io/en/2018/jetstream/boot.html,

• we should add at least a few talking about why cloud, why jetstream. why cloud? simplifies software install; can rent bigger machines as analysis needs scale; can scale to multiple machines. why jetstream? NSF XSEDE academic cloud, "free" with an allocation request. alternatives: amazon, google compute.
• we need to write and link in ssh login instructions, including key download; I think we were planning on doing Terminal for macs and Mobaxterm for Windows as defaults.

While things are booting: Introduction to collaboration tools: Slack, hackmd, and e-mail!). We should add talking points/text/screenshots:

• first! motivate / show / hand out stickies!

• slack is a way to do realtime passing around of notes / info during class

• it is also a good way to arrange/coordinate social activities; works on phones, etc.

• we will have room specific channels, as well as #general for course wide stuff and #random for fun.

• room specific channels can be used for questions during the presentation (instead of / in addition to asking for help)

• also have a #social channel, and maybe others; go ahead and invite.

hackmd:

• hackmd is a good way to do collaborative note taking
• will have one hackmd per room
• they will be persistent
• you are welcome to join us in taking notes! ask a TA or helper on how to connect in to edit instead of view

e-mail:

• will generally only be used for important updates and announcements of schedule changes
• schedule changes

For BLAST: https://angus.readthedocs.io/en/2018/running-command-line-blast.html

• should add a brief description of what BLAST does, and link out to longer descriptions
• add some talking points about "why command line" and promise that we'll get to command line training specifically. could take these from the top of the data carpentry genomics shell lesson, in brief? ("most bioinfo software runs at the command line, as you will see. this is for several reasons: history, remote computer usage, automation.")
• motivate: why are we working in a subdirectory?

For RSTudio, https://angus.readthedocs.io/en/2018/visualizing-blast-scores-with-RStudio.html:

• motivate usage of R. ("it's how we do actual exploratory data analysis. watch!") and explain that we'll do more R training over the next two weeks.
• tie back to command line: "you do the heavy lifting with file-based analysis at the shell, and then import the results into R and explore them there!"
• missing image/broken link in there...?
• would be good to link in some of the output of the R plotting so people can see it on their screen, although tell people we want them to follow along
• note that pdfs can be viewed through RStudio download interface, maybe add some screenshots with red circles and arrows pointing at how to get there

For QC etc. https://angus.readthedocs.io/en/2018/quality-and-trimming.html

• we should do an intro-to-Illumina-sequencing somewhere in here, as per @crazyhottommy comment
• I think we could use more talking points in here about what this all means, when you should and shouldn't trim harshly, etc. Or just be sure to invite lots of student comments and questions. In my experience this section could take a full session all on its own (~3 hours or more)

For mapping and variant calling, https://angus.readthedocs.io/en/2018/mapping-variant-calling.html

• need diagram/screenshot of what's going on!
• a discussion of "why so many steps in samtools" and "what else can you do with samtools?" would be good (e.g. getting reads for just a particular region of the genome).

For RNAseq, https://angus.readthedocs.io/en/2018/rna-seq.html

• we should put answers to some of the questions at the end into the document or instructor notes, maybe?

For RNAseq assembly, https://angus.readthedocs.io/en/2018/transcriptome-assembly.html:

• the learning objectives are in a weird format at the top?
• please check this lesson over for english :)
• maybe add some "how would we evaluate this transcriptome?" at the end. maybe do some blasts against the yeast ORFs from the rpevious lesson?
• have a wider discussion about busco - we could add a busco evaluation in here, might be useful (as optional if we have time)