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FunctionLab / sei-framework

code to run sei and obtain sei and sequence class predictions
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are the variant predictions done on positive strand sequences? #7

Closed okurman closed 2 years ago

okurman commented 2 years ago

Hi!

Sorry if I have missed this information somewhere in the publication, but I couldn't find it. I was wondering, are the variant scores done on positive strand sequences of SNPs when generated through the provided scripts?

Thanks!

jzthree commented 2 years ago

Sei prediction is not strand-specific (i.e. it uses both positive and negative strand sequences for prediction). The vcf file has to specify REF and ALT allele based on the '+' strand though.

okurman commented 2 years ago

Thank you! Just a follow-up question: if the input is run for both strands anyway, why do the REF/ALT have to be based on the + strand? Would the prediction scores be different depending on the strand of the REF/ALT?

jzthree commented 2 years ago

You cannot specify the strand in vcf format so using REF/ALT on + is the convention

okurman commented 2 years ago

Got it. Thank you!