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jldimond / jldimond-fish546-2016

FISH546 repository
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Week 4 Project Review #1

Open sr320 opened 7 years ago

sr320 commented 7 years ago

Here is a personalized video review

https://uw.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=a8cc97e9-49b0-4bd0-a023-aa310f51f106

Presume you are on moving forward with no major hurdles.

It would be nice to have a summary of the game plan for how you will tackle both sets of data, have a projected timeline, and associated links to where one could see major milestones. This would go on readme.

Nice Metadata table!

jldimond commented 7 years ago

Thanks for the comments. I am having a devil of a time getting GitHub desktop to do gitignores. It keeps freezing up on me. iPyrad creates lots of intermediate files that are very large, and I found it equally difficult to try to sync while the analysis was in progress.

sr320 commented 7 years ago

See http://d.pr/v/nPBR

Just edit gitignore in TextEdit. - keep a whole directory out... Lots of my big stuff I just write outside of the repo as it is 100GB and my computer does not even have room.

jldimond commented 7 years ago

Thank you, that worked!

jldimond commented 7 years ago

@sr320 - I am off for the next two weeks on vacation in Cuba. I may not have much access to the internet, so I have published the current version of my project on Zenodo (Figshare was not working). Here is the link:

https://zenodo.org/badge/latestdoi/70012703

The "knitted" R md files show all the analyses of the data and are most representative of the bulk of the work I did. Here are the paths for those files:

analyses/ipyrad_analysis/data3_outfiles/EpiRAD_analysis.md analyses/ipyrad_analysis/data3_outfiles/ddRAD_analysis.md

jldimond commented 7 years ago

Also, just so you know where I stand with this project. I am mostly happy with it as is, but I was able to collect some naturally bleached specimens that I think would make excellent reference samples to generate a symbiont-free assembly. So I hope to do a second round of ddRAD/EpiRAD this winter that will include those samples, plus some others.