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datacarpentry / organization-genomics

Project Organization and Management for Genomics
https://datacarpentry.org/organization-genomics
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Rewrite of the NCBI data locating #103

Closed hoytpr closed 5 years ago

hoytpr commented 5 years ago

After going through the lesson, the numbers didn't match up and it would be confusing to show the BioProject Number (PRJNA294072) from the paper, then go directly to SRP064605 of the Run Accessory Table (which is actually the SRA Run Selector Table) which has a DIFFERENT PRJNA number (i.e. PRJNA295606). This re-write shows the detailed process of going through the data located at BioProject "PRJNA294072" in the paper to the actual data used in this lesson. It also gives the instructor an opportunity to "skip" this section if time is short. Commit 233144b is the important one, others are mostly formatting the images. Comments from @taylorreiter , @tobyhodges are welcome.

ErinBecker commented 5 years ago

Wow! This is a lot of work - thank you @hoytpr for tracking down this issue and putting in a solution.

ErinBecker commented 5 years ago

@hoytpr - I'm just giving these changes a read through now. I'd highly recommend not keeping a "backup" version of the episode as it will make things more confusing for contributors down the road and make the file structure unnecessarily messy. It's ok to delete the old file and replace with the rewrite. if we need to go back to an earlier version, we can use the GitHub history.

hoytpr commented 5 years ago

Thanks for the heads up @ErinBecker!!! I am (destined to be) a life-long learner, and keeping a backup version of any .md file is definitely a thing NOT to do.

ErinBecker commented 5 years ago

@hoytpr - I've been "guilty" of this myself in the past. We're all life-long learners here! I'll give this another review now.

ErinBecker commented 5 years ago

@hoytpr - Thank you again for all of this great work! This is a fantastic addition to the lesson and I think will really help with some of the "flow" issues that have been identified with this lesson in previous workshops. I like that you've added solutions to the exercises as well. I've left some line by line comments and suggestions. Please let me know if you have any questions about my comments or would prefer me to put in a PR myself to address them. I'm looking forward to seeing your changes incorporated into the lesson!

hoytpr commented 5 years ago

Thanks very much @ErinBecker for this great feedback. Sorry for the number of PR versions, It's particularly ironic because I'm a proponent of NOT using gh-pages for commits and PRs. I will be moving back to using local rendering today if we can get things merged.

hoytpr commented 5 years ago

Thanks for everyone's patience with this effort. No more contributions are anticipated with this PR.

ErinBecker commented 5 years ago

Thanks for making those changes @hoytpr. This all looks good to me now. Merging!