Changes

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 --rerefence reference.fa --windowsize winsize --create_gc reference.gc

  qplot --refence reference.fa --windowsize winsize --create_gc reference.gc

''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.'''