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, 11:42, 16 February 2012
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| qplot --rerefence reference.fa --windowsize winsize --create_gc reference.gc | | qplot --rerefence reference.fa --windowsize winsize --create_gc reference.gc |
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− | ''Note'': Before running qplot, it is critical to check how the chromosome numbers are coded. Some bam files use just numbers, others use chr + numbers. '''You need to make sure that the chromosome numbers from the reference and dbSNP are consistent with the bam file.''' | + | ''Note'': Before running qplot, it is critical to check how the chromosome numbers are coded. Some BAM/SAM files use just numbers, others use chr + numbers. '''You need to make sure that the chromosome numbers from the reference and dbSNP are consistent with the BAM/SAM file.''' |
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| == Parameters == | | == Parameters == |