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JasonJWilliamsNY / abstracts

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some suggestions based on my own experience #1

Open crazyhottommy opened 6 years ago

crazyhottommy commented 6 years ago

Hi Jason,

Looking forward to see your presentation. I have several suggestions:

  1. Naming the files. This is the number 1 lesson everyone should learn. see a PPT by Jenny Bryan.

  2. beware that excel can make mistakes: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1044-7

and it is hard to parse if the entries are not entered properly and those (e.g.highlighting) formatted things can be a barrier to read into R/python.

  1. data cleaning skills data janitor work costs most time in a data project. https://www.nytimes.com/2014/08/18/technology/for-big-data-scientists-hurdle-to-insights-is-janitor-work.html

  2. Project organization/automation organize your project to make your work more reproducible. use R project if you use Rstudio. and have a folder structure.

some refs: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000424 https://www.biorxiv.org/content/early/2017/07/24/167619 https://arxiv.org/abs/1609.00037

A really nice one on sequencing data project https://www.biorxiv.org/content/early/2017/08/29/136358

I have some other notes https://github.com/crazyhottommy/getting-started-with-genomics-tools-and-resources#automate-your-workflow-open-science-and-reproducible-research

Tommy

JasonJWilliamsNY commented 6 years ago

Thanks will definitely look to comment om these kinds of issues!