The recommended gene expression (RNA-seq) scorers, GeneMaskLFCScorer

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1

I’m planning to calculated the effect of variants on gene expression, and I use GeneMaskLFCScorer as scorer. When I filtering variants which causing two-fold increase in gene expression, is it appropriate to set the raw_score threshold greater than 0.301 (i.e. log2) ?

Looking forward to your reply. Thank you very much.

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2

Hello,

Thank you for reaching out. For RNA_SEQ variant scorers we use a natural log transformation of the fold-change. So for a 2-fold change, you should use log(2) = 0.69314718.

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