I have a NGS data for whole genome of an organism. Actaully we did error prone PCR (eP PCR) for the whole genome. The Data we got have all the trans versions and transitions after error prone PCR. Now I want to calculate the number of unique variants possible after the error prone PCR. Pedel AA is our software of choice. But first we do not have the mutated genome sequence( after ep PCR).The data we get have only wild type sequence.
The result file we have contains all the substitutions possible, but we do not have mutated sequence. Second we do not have the mean number of nucleotide substitutions per daughter sequence which is an important input parameter for Pedel AA.
If we had done the capillary sequencing, we would have a mutated genome sequence after ep PCR and also we could have easily calculated the mean mean number of nucleotide substitutions per daughter sequence.
Kindly help me and let me know how we can calculate the mean number of substitutions per daughter sequence from this NGS data, which have given only wild type sequence.
Thanks
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working on such issues!
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