Last practicals issues

[yannickwurm]

Random order, sorry

• ", which makes variant calling easier." -> add. Bacteria and yeast are typically also haploid. The same is true for most of the genome for highly-inbred strains of laboratory organisms.
• To reduce confusion, lets consistely use zless instead of zcat
• Several students had difficulty creating a bowtie index doesnt work with linked fasta?
• title "Pipeline" should encompass the implementation of one step, not just part of it
• Graphs for Fst should be connected lines.
• -- should add a step to say delete your .sam files! (or entire tmp folders) #88
• Authors byline at the top isn't really relevant anymore

[yeban]

bowtie index works with linked fasta

[yeban]

Several students had difficulty creating a bowtie index doesnt work with linked fasta?
> bowtie index works with linked fasta

The specific problem there, I think, is that the symlink command is given (ln -s ~/2020-10-xx-mapping/input/reference.fa tmp/) which students copy-paste as it is without replacing the xx, ending up with a broken symlink. Options, in my opinion, are:

1. add a message saying replace xx
2. use year-month timestamp throughout

[yannickwurm]

@aswitwicka @gabrielluishernandez @MPriebe - please feel free to address this and other issues in the 2021 GitHub issues prior to the semester starting and while there is plenty of time to spare

[yannickwurm]

@gabrielluishernandez are these resolved?
(re the broken link - if not yet done - add a message saying "if something doesn't seem to be working correctly, check that the files you are telling the computer to work with contain what you think they should contain"