shell-genomics
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Introduction to the Command Line for Genomics
I believe it is a little abrupt to go from "this is grep" to assessing read quality using grep. I wonder if an example just using the general nucleotides would...
The lesson demonstrates `cat` by applying `cat` to a fastq file. Can we `cat` a different file instead? When the learners go back to working with full size fastq files,...
In the exercise Finding hidden directories, `ls -a` will output `. .. .hidden sra_metadata untrimmed_fastq` to the terminal. I think that leaving the `.` and `..` there without explanations might...
In the fastqc part of the data wrangling we have folks download data (and learners usually want to know how to download things anyway). I'm wondering if there is an...
Showing `rm -i` in the lesson would be a nice option instead of just `rm`. Many users learning `rm` for the first time probably get the *be very very careful*...
Arizona Bug BBQ - In general we dislike the current set of exercises using grep. it is quite artificial and not relevant to the pipeline that we are working through...
After explaining the permission files concept and showing how to use it to protect your files as #223 suggests, a student asks how would you change the other premissions. The...
…ing edits to files The command ls -lh is a great way for learners to feel more confident that they are not working with corrupt files during their analysis.
For the Introduction to the Command Line for Genomics, Navigating Files and Directories I tried to use the material as the teaching demo, I found it will be better if...
Not a huge issue but this lesson uses pscp, while the genomics lessons use scp. Some consistency would be better.
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Introduction to the Command Line for Genomics