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SeqShop: Aligning Your Own Genome, December 2014 (view source)

Revision as of 15:44, 6 December 2014

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== First Things First ==
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*Helpful reference to many tools:
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** http://infoplatter.wordpress.com/2014/04/06/bioinformaticians-pocket-reference/
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*** links to "cheat-sheets", including, Unix, screen, and vi
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* Our wiki with some brief description of how to do some basic commands
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**http://genome.sph.umich.edu/wiki/Basic_Linux_Intro
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* [[Screen Commands]] for commands to use screen (one way to leave your commands running even after you log out)
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== Goals of This Session ==
 
== Goals of This Session ==
 
Learn how to go from your FASTQ files to generate Aligned BAMs.
 
Learn how to go from your FASTQ files to generate Aligned BAMs.
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* Practice setting up and running GotCloud on your own.
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* '''Your samples have already been aligned''', so we will review the steps that were done
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** Workshop computers don't have enough compute to align everyone's samples during the workshop
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* You will get to take home both the original FASTQs and the aligned BAMs on a USB drive
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** You will get it by the end of the week if not before - it takes a while to copy 74G-111G.  
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** 4 samples will get BAMs with "binned" qualities so both FASTQ & BAM would fit on the drive
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*** In future all generated BAMs will be automatically binned.
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** Those that didn't get sequenced will get a drive with NA12878 public sample on it
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{{SeqShopLogin}}
 
{{SeqShopLogin}}
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/12122"

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