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piquelab / QuASAR

Quantitative Allele Specific Analysis of Reads. Joint genotyping & ASE inference for RNA-seq data
MIT License
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What if there is only one sample per individual? #14

Open plbngl opened 6 years ago

plbngl commented 6 years ago

Hello, does quasar work even if there is only one bam file? How would the workflow work? Thank you!!

hbliu commented 2 years ago

Please try following code (which works for me) if one sample for each individual: ase.dat <- UnionExtractFields(fileNames) ase.dat.gt <- PrepForGenotyping(ase.dat, min.coverage=5) str(ase.dat.gt) ase.dat.gt$ref <- as.matrix(ase.dat.gt$ref); colnames(ase.dat.gt$ref) <- c("Sample") ase.dat.gt$alt <- as.matrix(ase.dat.gt$alt); colnames(ase.dat.gt$alt) <- c("Sample") sample.names <- colnames(ase.dat.gt$ref)