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, 12:49, 23 October 2014
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| | = Using Your own Reference Files = | | = Using Your own Reference Files = |
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| − | == Human Reference ==
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| − | === Generating BWA Reference Files ===
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| − | Use "bwa index" to generate the human reference files with the required extensions:
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| − | * .amb
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| − | * .ann
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| − | * .bwt
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| − | * .pac
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| − | * .sa
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| − | See http://bio-bwa.sourceforge.net/bwa.shtml for more information about using "bwa index".
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| − | === Generating Reference Index Files ===
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| − | Use "samtools faidx" to generate the human reference files with the required extensions:
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| − | * .fai
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| − | === Generating GC Content File ===
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| − | The GC Content file is used by QPLOT. It is assumed to be at the same location as the reference file.
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| − | If the reference file is at path/ref.fa, the GC Content file is expected to be:path/ref.winsize100.gc
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| − | To generate the GC content file, run qplot:
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| − | GOTCLOUD_DIR/bin/qplot --reference reference.fa --winsize windowSize
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| − | * Replace reference.fa with the name of your human reference fasta file.
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| − | * Replace windowSize with your desired window size, or leave out --winsize to use the default (100).
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| − | NOTE: You will get an error at the end of qplot that says:
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| − | <pre>
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| − | FATAL ERROR -
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| − | No SAM/BAM files provided, stopped!
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| − | </pre>
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| − | This error is due to using qplot to just generate a GC Content file and not also process a BAM file.
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| − | But it was successful as long as you see (where reference is the name of your reference file):
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| − | <pre>
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| − | GC content file [ reference.winsize100.gc ] created.
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| − | </pre>
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| − | See [[QPLOT#Input_files|QPLOT: InputFiles]] for more information.
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