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19 bytes removed
, 10:07, 6 January 2014
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| * Index file - See the example index file already prepared for this project | | * Index file - See the example index file already prepared for this project |
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− | cat $S5/examples/index/chr7.CFTR.fastq.index | + | cat $S5/examples/index/chr7.CFTR.fastq.index |
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| * Configuration File - See the example configuration file below. | | * Configuration File - See the example configuration file below. |
− | % cat $S5/examples/index/chr7.CFTR.align.conf� | + | cat $S5/examples/index/chr7.CFTR.align.conf |
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− | �INDEX_FILE = index/chr7.CFTR.fastq.index | + | INDEX_FILE = index/chr7.CFTR.fastq.index |
| ################### | | ################### |
| # References | | # References |
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| Default options should be mostly fine in many other cases. In this example, because it is not genome-wide calling, reference files are modified to be chr7-specific | | Default options should be mostly fine in many other cases. In this example, because it is not genome-wide calling, reference files are modified to be chr7-specific |
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| === Run GotCloud Alignment Pipeline === | | === Run GotCloud Alignment Pipeline === |
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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 === |