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, 13:45, 17 June 2013
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| Although GC content can be calculated on the fly each time, it is much more efficient to load a precomputed GC content from a file. To generate the file, use the following command: | | Although GC content can be calculated on the fly each time, it is much more efficient to load a precomputed GC content from a file. To generate the file, use the following command: |
− | qplot --refence reference.fa --windowsize winsize --create_gc reference.gc | + | qplot --reference reference.fa --windowsize winsize --create_gc reference.gc |
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| ''Note'': Before running qplot, it is critical to check how the chromosome names are coded. Some BAM/SAM files use just numbers, others use chr + numbers. '''You need to make sure that the chromosome names from the reference and dbSNP are consistent with the BAM/SAM files.''' | | ''Note'': Before running qplot, it is critical to check how the chromosome names are coded. Some BAM/SAM files use just numbers, others use chr + numbers. '''You need to make sure that the chromosome names from the reference and dbSNP are consistent with the BAM/SAM files.''' |