Model_ddPCR_underestimation_V2.sh will run the simulaiton while Run_model_ddPCR_underestimation_V2.sh is a wrapper for running the simulation n times. When done, run Summarise_ddPCR_underestimation.sh to create a summary table.
| Column | Description |
|---|---|
| # Genomes | Number of analysed genomes |
| # Frags per genome | Number of fragments generated per genome |
| Frags w. SSU | Number of total fragments with one or more SSU genes in them |
| P frags w. SSU | Fraction of Frags w. SSU / # Genomes * # Frags per genome |
| Frags w. PCR | Number of total fragments with one or more PCR hits in them |
| P frags w. PCR | Fraction of total fragments with one or more PCR hits in them |
| Frags w. multi SSU | Number of total fragments with multiple SSU genes in them |
| P frags w. multi SSU | Fraction of total fragments with multiple SSU genes in them |
| Frags w. multi PCR | Number of total fragments with multiple PCR hits in them |
| P frags w. multi PCR | Fraction of total fragments with multiple PCR hits in them |
| P SSU frags with PCR | Fraction of PCR hits in total number of fragments with SSU |
| P multi PCR | Fraction of multiple PCR hits in total number of fragments with a PCR hit |
| Corrected ddPCR value | Number of true SSU genes in all fragments from all genomes |