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Revision as of 22:27, 7 December 2014
, 22:27, 7 December 2014→Alignment Pipeline Output
== Alignment Pipeline Output ==
== Alignment Pipeline Output ==
The output is in ~/Sample#/output
cd ~/Sample*/output
ls
What is there?
* '''bam.list''' - list of samples/BAMs (just one)
* '''bams''' - directory with BAM files
* Makefiles - makefiles generated when I ran GotCloud
* QCFiles - quality control metrics
** We will look at this later
Look at the BAM list (will be used for snpcall that we will start tomorrow)
cat bam.list
* sample(tab)bam
Look in the bams directory:
ls bams
=== Quality Control Output ===
ls QCFiles/
== FEEDBACK! ==
== FEEDBACK! ==
Please provide feedback on the lectures/tutorials from today: https://docs.google.com/forms/d/1HY9g_GzTZzwddA9bmoyG1IJBgKukk3ouVR5uBboydec/viewform
Please provide feedback on the lectures/tutorials from today: https://docs.google.com/forms/d/1HY9g_GzTZzwddA9bmoyG1IJBgKukk3ouVR5uBboydec/viewform
