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Revision as of 21:54, 7 December 2014
, 21:54, 7 December 2014→Locating your FASTQs
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== First Things First ==
When you see Sample*/Sample#, replace it with your sample name/number
* If you are using generic data, use NA12878
== Locating your FASTQs ==
== Locating your FASTQs ==
Your FASTQ files are under <code>~/Sample*/fastqs</code> directory.
Your FASTQ files are under <code>~/Sample*/fastqs</code> directory.
Look at your directory:
Look at your directory:
ls ~/Sample*/fastqs
ls ~/Sample*/fastqs
* <code>ls</code> does a directory listing
* <code>ls</code> does a directory listing
* <code>~/</code> means to start from your home/base directory
* <code>~/</code> means to start from your home/base directory
You will see 2 files:
You will see 2 files:
* Sample_R1.fastq.gz - 1st in pair
* Sample#_R1.fastq.gz - 1st in pair
* Sample_R2.fastq.gz - 2nd in pair
* Sample#_R2.fastq.gz - 2nd in pair
== What did I do to run the alignment? ==
== What did I do to run the alignment? ==
