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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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Wrong pre-processing allele frequency BED format #4

Closed MrFlick closed 9 years ago

MrFlick commented 9 years ago

In the main README, under the "Pileups & cleaned pileups" section, it says that the BED file should contain "1-3) coordinate, 4) SNP ID, 5) allele frequency". However, the sample R script that reads in the intersected data (convertPileupToQuasar.R) has columns for

names(pileup) <- c("chr", "pos-1", "pos", "ref", "num.reads", "read.alleles",
    "read.quality", "rsID", "TKG.Ref", "alt", "af")

So it looks like the BED file should actually have 7 columns: 1-3) coordinate, 4) SNP ID, 5) ref allele 6) alt allele 5) allele frequency

gmoyerbrailean commented 9 years ago

Thanks for pointing this out! I have updated the README to reflect how this file should be formatted.