Hello,
I'm currently designing a pipeline for allele-specific expression analysis. I was wondering if it made sense to compare the allelic ratios at heterozygous snps coming from RNAseq with the allelic ratio from DNA sequencing, as to check for false allelic imbalances due to amplification bias. I hadn't seen any articles mentioning this until yesterday (https://www.nature.com/articles/s41598-020-79990-9#Sec8 and https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4832550/).
The difference in quality control processes between DNA and RNA sequencing and the assumption that there's an equal amplification bias make me doubt this comparison is feasible, and I don't understand what these articles meant to do.
Is this worth doing? What are your opinions? Any clarification would be much appreciated.
Thank you!
