calculate ratio between tumor and normal sample’s WGS read counts

[Bio-LiHe]

Hi

fragCounter using CBS algorithm calculate read couts ratio between tumor and normal sample in 200bp genomic bins.

I would like to ask which is the output parameter of the normal sample? This code doesn't see the input parameters of normal.

frag -b inst/extdata/chr21.bam -d inst/extdata/gcMAP21/ -w 200  

[zining01]

Yes, you're correct that fragCounter doesn't see the input parameters of the normal sample. You will need to run fragCounter on your tumo and normal BAM files separately, then compute the tumor/normal ratio afterwards by dividing reads.corrected per bin of the tumor sample by the normal sample.

Hope that makes sense!

[9421g]

Hi, my tumor/normal data has different sequencing depth.
Should I use (tumor.reads.corrected / tumor.mean_coverage) / (normal .reads.corrected / normal .mean_coverage)
instead of tumor.reads.corrected / normal .reads.corrected as you mention.

mean_coverage is from other tool.