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2016 Feb-May: Programming for Genomics

I am teaching BIOB491 Programming for Genomics in the Spring of 2016.
I will be posting announcements and assignments here as well as on Moodle so check back regularly for updates.
Here is a good beginners tutorial for UNIX: http://www.ee.surrey.ac.uk/Teaching/Unix/

Updates:

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28 January 2016
Due to some time conflicts, we will now be holding class at 2:40-4:00 on Tuesdays and Thursdays in HS114 (instead of 2:10-3:30).
My Office hours are Tuesday morning from 9-10 in HS114.

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1 February 2016
An interesting story is unfolding about a bioinformatics error. We'll discuss this later in class, but here's a couple quick links:
The original article:
      http://science.sciencemag.org/content/350/6262/820
The erratum notice:
     https://dl.dropboxusercontent.com/u/26978112/Erratum%20with%20figures.pdf
     --link broken, but you should be able to find the erratum at the science website.
Ewen Callaway on the original article:
     http://www.nature.com/news/first-ancient-african-genome-reveals-vast-eurasian-migration-1.18531
Ewen Callaway on the retraction:
     http://www.nature.com/news/error-found-in-study-of-first-ancient-african-genome-1.19258
A couple good blog posts about everything:    
     https://whyevolutionistrue.wordpress.com/2016/01/30/we-are-not-all-neanderthal-this-is-how-science-proceeds/
     http://www.opiniomics.org/bioinformatics-error-responsible-for-retraction-in-science/

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24 March 2016
It's a couple years old, but it's a very worthwhile read:
29 March 2016

Here is the large (3GB) fastq file for you to test HW8_P6 on:
--The link is now broken, please email me for access

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HW1.zip
(5k)
Tom Brekke,
Jan 28, 2016, 8:08 PM
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HW10_P8.txt
(1k)
Tom Brekke,
Apr 19, 2016, 8:26 AM
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HW2.zip
(36k)
Tom Brekke,
Feb 9, 2016, 12:58 PM
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HW3_P1.txt
(2k)
Tom Brekke,
Feb 17, 2016, 9:08 AM
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HW4_P2.txt
(1k)
Tom Brekke,
Feb 25, 2016, 3:26 PM
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HW5_P3.zip
(27k)
Tom Brekke,
Mar 1, 2016, 7:21 PM
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HW6_P4.zip
(44k)
Tom Brekke,
Mar 10, 2016, 4:49 PM
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HW7_P5.zip
(44k)
Tom Brekke,
Mar 17, 2016, 5:32 PM
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HW8_P6.zip
(23k)
Tom Brekke,
Mar 24, 2016, 4:32 PM
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HW9_7.txt
(1k)
Tom Brekke,
Apr 19, 2016, 8:27 AM
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Tom Brekke,
Jan 28, 2016, 12:02 PM
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REGEX_List.txt
(2k)
Tom Brekke,
Jan 28, 2016, 4:19 PM
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Useful_Bash_Commands.txt
(1k)
Tom Brekke,
Feb 4, 2016, 7:49 PM
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