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GotCloud: Alignment Pipeline (view source)

Revision as of 23:56, 20 February 2013

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= Mapping Pipeline =
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Back to parent: [[GotCloud]]
 
Back to parent: [[GotCloud]]
    
The Mapping Pipeline takes FASTQ files and generates recalibrated BAM files from them.
 
The Mapping Pipeline takes FASTQ files and generates recalibrated BAM files from them.
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== Running the GotCloud Mapping Pipeline ==
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The mapping pipeline is run using the <code>gen_biopipeline.pl</code> script found in the <code>bin/</code> directory under the <code>gotcloud/</code> installation.
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===Running the Automatic Test===
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The automatic tests run GotCloud on small testsets and check the results against expected results validating that GotCloud is installed correctly.
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*Run alignment pipeline test:
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gen_biopipeline.pl --test OUTPUT_DIR
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where OUTPUT_DIR is the directory where you want to store the test results
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If you see "Successfully ran the test case, congratulations!", then you are ready to align samples.
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== Overview of Mapping Pipeline Steps ==
 
Here is an overview of the Mapping Pipeline:
 
Here is an overview of the Mapping Pipeline:
  
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/6478"

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