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wyang17 / SQuIRE

Software for Quantifying Interspersed Repeat Expression
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Normalization #84

Open helenhuangmath opened 2 years ago

helenhuangmath commented 2 years ago

Hello,

I'm wondering which normalization would you suggest to use? Should I use full "alignedsize" (this should be sum of all reads of gene and TEs if I understand correctly), or should I use sum of "tot_counts" (which I assume is TE reads)?

Thank you!

helenhuangmath commented 2 years ago

Continue to the question above, which normalization way does SQuIRE call step use?

Thank you!