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cancerit / NanoSeq

Analysis software for Nanorate Sequencing (NanoSeq) experiments
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Source of human genome trinucleotide frequencies #78

Closed gevro closed 11 months ago

gevro commented 11 months ago

Hi, For calculation of ratio2genome in the results, what reference version of the human genome are the below counts? It seems closer to hg38 than hg19 from my analysis.

Thanks!

  # human genome trinucleotide frequencies assumed
  genome_counts = vector()
  genome_counts[c("ACA", "ACC", "ACG", "ACT", "ATA", "ATC", "ATG", "ATT", "CCA", "CCC", "CCG", "CCT", "CTA", "CTC", "CTG", "CTT",
                  "GCA", "GCC", "GCG", "GCT", "GTA", "GTC", "GTG", "GTT", "TCA", "TCC", "TCG", "TCT", "TTA", "TTC", "TTG", "TTT")] =
                  c(115415924, 66550070, 14381094, 92058521, 117976329, 76401029, 105094288, 142651503, 105547494, 75238490,
                    15801067, 101628641, 73791042, 96335416, 115950255, 114180747, 82414099, 68090507, 13621251, 80004082,
                    64915540, 54055728, 86012414, 83421918, 112085858, 88336615, 12630597, 126566213, 119020255, 112827451,
                    108406418, 219915599)
fa8sanger commented 11 months ago

I obtained those from the deconstructSigs R package

On 25 Nov 2023, at 20:03, gevro @.***> wrote:

Hi, For calculation of ratio2genome in the results, what reference version of the human genome are the below counts? It seems closer to hg38 than hg19 from my analysis.

Thanks!

human genome trinucleotide frequencies assumed

genome_counts = vector() genome_counts[c("ACA", "ACC", "ACG", "ACT", "ATA", "ATC", "ATG", "ATT", "CCA", "CCC", "CCG", "CCT", "CTA", "CTC", "CTG", "CTT", "GCA", "GCC", "GCG", "GCT", "GTA", "GTC", "GTG", "GTT", "TCA", "TCC", "TCG", "TCT", "TTA", "TTC", "TTG", "TTT")] = c(115415924, 66550070, 14381094, 92058521, 117976329, 76401029, 105094288, 142651503, 105547494, 75238490, 15801067, 101628641, 73791042, 96335416, 115950255, 114180747, 82414099, 68090507, 13621251, 80004082, 64915540, 54055728, 86012414, 83421918, 112085858, 88336615, 12630597, 126566213, 119020255, 112827451, 108406418, 219915599)

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