Can we assume that the mutations with pyrimidine strand column equals 0 are originally from the reference strand (positive strand) of the genome?

AlexandrovLab / SigProfilerMatrixGenerator

SigProfilerMatrixGenerator creates mutational matrices for all types of somatic mutations. It allows downsizing the generated mutations only to parts for the genome (e.g., exome or a custom BED file). The tool seamlessly integrates with other SigProfiler tools.

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Can we assume that the mutations with pyrimidine strand column equals 0 are originally from the reference strand (positive strand) of the genome? #202

Closed burcakotlu closed 2 weeks ago

burcakotlu commented 2 weeks ago

Dear all,

SPT uses the pyrimidine strand column of the mutation after SPMG call for replication strand asymmetry analyses. However, the pyrimidine strand is 0 for some doublets and indels which contain both pyrimidine and purine bases. Can we consider that such mutations are originally from the reference strand which is the positive strand of the genome?

Thanks, Burcak

mdbarnesUCSD commented 2 weeks ago

Dear @burcakotlu,

In cases for doublet bases substitutions and indels, when there is a mix of purines and pyrimidines then the pyrimidine reference strand can not be determined so the value is "0". For positives with only purines or only pyrimidines, the strand is a "1" when that mutation is on the reference strand and is "-1" when it is reverse complement of the reference strand.