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, 03:31, 6 January 2014
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| * Using the prepared input files, align the FASTQ files using the gotcloud alignment pipeline | | * Using the prepared input files, align the FASTQ files using the gotcloud alignment pipeline |
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− | $S5/gotcloud/gotcloud align �--conf $S5/examples/index/chr7.CFTR.align.conf� --outDir ~/out/align --baseprefix $S5/examples | + | $S5/gotcloud/gotcloud align --conf $S5/examples/index/chr7.CFTR.align.conf --outDir ~/out/align --baseprefix $S5/examples |
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| * Check if the output BAMs and QC metrics are produced | | * Check if the output BAMs and QC metrics are produced |
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− | ls ~/out/align/bams� | + | ls ~/out/align/bams |
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− | ls ~/out/align/QCFiles/� | + | ls ~/out/align/QCFiles/ |
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| === Understanding the Output Files === | | === Understanding the Output Files === |