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Tutorial: EMMAX GotCloud STOM: Lecture 5

12 bytes removed, 02:31, 6 January 2014
Run GotCloud Alignment Pipeline
* Using the prepared input files, align the FASTQ files using the gotcloud alignment pipeline
$S5/gotcloud/gotcloud align --conf $S5/examples/index/chr7.CFTR.align.conf� conf --outDir ~/out/align --baseprefix $S5/examples
* Check if the output BAMs and QC metrics are produced
ls ~/out/align/bams�bams
ls ~/out/align/QCFiles/
=== Understanding the Output Files ===

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