I have previously tested for allele-specific expression in paired samples with DESeq2 (like so), but also would like to set up contrasts of ASE across conditions where the sample individual cannot be represented twice. Specifically, I have a dataset where tissue was collect under two treatments (hot v. cold) and would like to identify cases of ASE that are treatment specific. However, since tissues cannot be collected for the sample sample under both "hot" and "cold", I have not been able to get around the issue of this not being a "full rank design"
My condition design table is something like this (with 6 reps of each treatment, so 12 alleles):
ID treatment sample allele ill98 Warm 1 ref ill98 Warm 1 alt ill97 cold 2 ref ill97 cold 2 alt
Appreciate any guidance on how to set this up in DESeq2 or whether using DESeq2 isn't possible for this purpose! Thank you!