Erin Becker comments

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                                            Erin Becker

Episode 03: Working with Files and Directories -- cat something other than a fastq file

Thanks for thinking of how this would affect later lessons @aschuerch. I've just done a search in those two lesson repos and found that `cat` is used multiple times in...

sftp transfer software

Thanks for putting in this issue @sstevens2! The Maintainers for this lesson will be meeting on Friday and will try to offer some suggestions here. I'd love to also get...

sftp transfer software

@sstevens2 - I think we had FileZilla in the lesson for a while but removed it. I don't remember why. Maybe one of the @datacarpentry/shell-genomics-maintainers can share some history and...

Explain filtering variants and show its effects with the TS/TV ratio.

Thank you for this contribution @rcastelo! This is a nicely worded explanation of the filtering option in `bcftools`. As these lessons are already quite full, I would recommend not incorporating...

Explain filtering variants and show its effects with the TS/TV ratio.

@vlrieg - Done! Please go ahead and merge this if you're happy with it. Use "merge pull request" rather than "squash and merge" to ensure @rcastelo's original commit gets counted.

adding "command --help" to 01-introduction lesson...or to the cloud lessons

I'm setting up the agenda for the CAC, which will meet on 24 and 25 September. I will add to their agenda the question of the order of the shell...

Add locations of true and false positive variant calls

@lexnederbragt - this is a great idea but I think will have to wait for our next lesson release.

change quality encoding scale in 02 Assessing Read Quality

#127 has merge conflicts. Any volunteers to fix that up? 😄

shell-genomics/05-writing-scripts

Thanks @JasonJWilliamsNY and @aschuerch for this discussion. Adding https://github.com/datacarpentry/shell-genomics/pull/201 here as cross-ref.

shell-genomics/05-writing-scripts

Thanks all for this discussion. I second @ACharbonneau's comments about the current focus of the cloud lesson and that moving the scp section back to cloud would break the flow...