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Other settings of STAR remained at default settings.
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For sensitivity analysis, each parameter value is changed at once, while other parameters remain at default value.
The story does not change, and original enemy statistics will remain at default.
The selected assembly parameters used an expected coverage value of 40X with all other settings remaining at default values.
With all other parameters remaining at default values, the methods of Rudge et al. [ 29] indicate that the optimal composition of a Zn Zn DS is Zn/Zn = 4.88, which differs from the composition chosen for this study (Zn/Zn ≈ 2.51); however, the effect on error propagation and the range of optimal spike sample ratios is small (Fig. 1).
The option for a negative matrix was turned on, while the other parameters remained at the default setting.
All other WGCNA parameters remained at their default settings.
Blast2GO parameters were set as follows: E-Value-Hit-Filter < 1e-6; annotation cutOff = 55; other parameters remained at the default values.
In the mentioned tool, the maximum free energy threshold for the folded structures was set at -18 kcal/mol, while the other parameters remained as default.
Most parameters remained as default values.
All other parameter priors remained as default values (10 10 000).
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