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Common stuff:
Credentials
- Projector: Code 1988
- Workstations: student hookem
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- Make sure you source the common profile, or if not, be sure to execute umask 002 to make all files you create group writable.
- If your primary group is not the NGSC group, do this right after logging so that all files you create will be the NGSC group (G-803889)
Code Block newgrp - G-803889 umask 002
Instructors de-briefing
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5/23/13:
- Most common confusion in tutorials:
- local computer vs TACC vs idev
- where example commands are being executed (current directory)
- 1st day overwhelming for non-Unix folks (as usual). Maybe find a way to introduce commands as part of guided lecture?
- Three kinds of sections from us: 1) lecture 2) guided lecture (they exec some cmds) 3) tutorial
- Have more 1 & 2 early on, moving to more 2 & 3 as they get more comfortable
- Definitely go through mapping tutorial one step at a time from the front of the class - this should be REALLY clear
- Should explore full day for TopHat - maybe yeast in TopHat? More interactive demos on graphing, etc. Theoretically (in Anna's mind) this is already done!
- Maintain encouragement to the linux-challenged
- Maybe an assembly evaluation tool?
- Maybe switch from a genome assembly to a transcriptome assembly (i.e. the yeast subset from the TopHat)
- Should move to bowtie2
- Need to clarify language: reference, reference genome, indexes (references, bam files)
- Need to clarify "commands" file (for launcher_creator.py) vs a bash script
- Fix wrap-around with "nowrap" macro instead of "code" macro
- Maybe some "speciality" or niche application exposure - metagenomics, IMGT, ddRAD analysis, etc.
- Should we describe library prep more? Or things like enrichment?
- It was good to have expanded QC discussion.
- Maybe manipulatives.
Instructors de-briefing 8/23/12:
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