What if I dont have allele frequency in a population?

piquelab / QuASAR

Quantitative Allele Specific Analysis of Reads. Joint genotyping & ASE inference for RNA-seq data

MIT License

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What if I dont have allele frequency in a population? #12

Open lss1227 opened 7 years ago

lss1227 commented 7 years ago

I want to infer ASE but not from human. My sample is small to form a population. Can I use QuASAR? Thank you very much !

sergiopalmavera commented 7 years ago

I am having the same problem. I am keen to hear some suggestions

michaelcvermeulen commented 6 years ago

I have a similar question. What allele frequencies is the program designed to input? The provided 1KG SNP file has a column for "global allele frequency" but many of the sites are greater than 0.5. If I am inputting a custom bed of SNPs what allele frequencies do I use? I would assume global allele frequency is analogous to global minor allele frequency and I have that data.