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mskilab-org / fragCounter

GC and mappability corrected fragment coverage for paired end whole genome sequencing
MIT License
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calculate ratio between tumor and normal sample’s WGS read counts #24

Open Bio-LiHe opened 1 year ago

Bio-LiHe commented 1 year ago

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 commented 1 year ago

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!