I am a student doing a research project in allele-specific expression,
and am planning to use your lab’s AlleleSeq tool.
I am trying to use the YRI Population HapMap data. I went and tried to
find phased YRI trio data (from 1000 Genomes) to input into the
vcf2diploid tool. Unfortunately, I found data that includes only the
parent ID’s, but not the child’s. Since I don’t have the child data, I
am unable to use the AlleleSeq pipeline.
I was wondering if you could give me some suggestions on how to do ASE
given only the parental data.
Thank you for your interest in the AlleleSeq pipeline.
The AlleleSeq pipeline assumes that the ‘child’ is the subject in which you
are trying to find ASE. Hence the genotypes of the subject are required.