Fitness score

[eric-jm-lang]

Hello,
Thank you very much for sharing ECNet with the scientific community.
Could you please provide more information about the 'Fitness Score' which is required in the Fitness TSV file and quantifies the variant's fitness.
In particular, could you please let me know how it is calculated and how one would calculate the fitness score for one's own mutagenesis data?
Are there examples from the litterature that define this score and/or programs that facilitate its calculation?
Many thanks in advance

[luoyunan]

Hi, Thanks for the great question! The definition of fitness score depends on the property one wants to measure. ECNet uses the fitness scores defined in the original reference. In the literature, the fitness score is typically defined as the (log-transformed) ratio of read counts before and after selection. Here are a few related papers:
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02091-3
https://www.nature.com/articles/s41588-019-0431-x
https://www.nature.com/articles/s41588-019-0432-9