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Tutorial: EMMAX GotCloud STOM: Lecture 5

12 bytes removed, 10:07, 6 January 2014
Preparing Input Files
* Index file - See the example index file already prepared for this project
cat $S5/examples/index/chr7.CFTR.fastq.index
* Configuration File - See the example configuration file below.
% cat $S5/examples/index/chr7.CFTR.align.conf
INDEX_FILE = index/chr7.CFTR.fastq.index
###################
* 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 ===