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Although GC content can be calculated on 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 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 --rerefence reference.fa --windowsize windowSize --gc reference.gc
qplot --rerefence reference.fa --windowsize windowSize --create_gc reference.gc
''Note'': Before running the qplot, it is critical to check how the chromosome numbers are coded. Some bam file use just numbers, others use chr + numbers. '''You need to make sure that the chromosome numbers from reference and dbsnp are consistent with the bam file.'''
''Note'': Before running the qplot, it is critical to check how the chromosome numbers are coded. Some bam file use just numbers, others use chr + numbers. '''You need to make sure that the chromosome numbers from reference and dbsnp are consistent with the bam file.'''
