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[quiz] Completed workflow #22

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sr320 opened this issue Jan 26, 2015 · 8 comments
Closed

[quiz] Completed workflow #22

sr320 opened this issue Jan 26, 2015 · 8 comments
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@sr320
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sr320 commented Jan 26, 2015

What is the url to your completed workflow? This can be in draft state but you need to a page where you go from start to finish. Does not have to be perfect and can even include Excel at this point....
If you need help recalling what you should be doing, see this.

@sr320 sr320 added the quiz label Jan 26, 2015
@jheare
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jheare commented Jan 28, 2015

I've created a Workflow for STACKS labeling the function, process, and output of every step. I've also included a basic guide for what everything does and why its important or why we chose certain options. It includes a summary of the entire process at the end. It will be updated as I work on the data.

You can see the workflow here.

@willking2
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@sr320
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sr320 commented Jan 28, 2015

Please note this 'workflow' needs to be a document that someone else could use to replicate your work and get the same result.

Double Point Bonus 👆 ✖️ 👆 for first one in..

@kubu4
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kubu4 commented Jan 29, 2015

We discussed this quiz question in class and I think we're all confused on what exactly this means. How does this differ from the methods.md we wrote?

@sr320
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sr320 commented Jan 29, 2015

So this should be markdown file, IPython nb, etc that documents
bioinformatic workflow in a manner which the work could be reproduced.

For example
http://nbviewer.ipython.org/github/sr320/eimd-sswd/blob/master/eimd_analysis.ipynb

Main point is showing steps how raw data is analyzed to get final product
(ie list of genes, annotated transciptome etc).

@sr320 sr320 modified the milestone: Week4 Jan 29, 2015
@jldimond
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http://nbviewer.ipython.org/github/jldimond/fish546-2015/blob/master/nb/CpG_ratio_graph_Ahya.ipynb

My progress on this was hampered by SQLshare not allowing me to download any of my datasets this afternoon. What is up with that?:thumbsdown:

@kubu4
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kubu4 commented Jan 30, 2015

Whoa! You have graphs! 👍

Any error message that you received from SQLShare regarding the downloads failing?

@sr320
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sr320 commented Jan 30, 2015

Related - show the error in your notebook so we can troubleshoot. 

In this case screenshots are handy.

You can also give us url directly to section in notebook.


Steven Roberts

On Thu, Jan 29, 2015 at 4:06 PM, kubu4 notifications@github.com wrote:

Whoa! You have graphs! 👍

Any error message that you received from SQLShare regarding the downloads failing?

Reply to this email directly or view it on GitHub:
#22 (comment)

@sr320 sr320 closed this as completed Feb 5, 2015
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