I want to use DESeq2 for assessing allele-specific expression. I will compare gene-level allelic counts of a yeast hybrid (basically comparing counts of orthologous genes of parentals of this hybrid).
I'm aware of this tutorial http://rstudio-pubs-static.s3.amazonaws.com/275642_e9d578fe1f7a404aad0553f52236c0a4.html.
My question is that parentals might have orthologous genes with different lengths, so for example ortholog in parent A is 1000bp and in parent B is 1020 bp. Is it possible at some step of DESeq2 to account for this length difference?
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If you provide a matrix at the beginning of the analysis called “avgTxLength”, the analysis will control for gene length changes across sample. This should happen before running DESeq().
assays(dds)[["avgTxLength"]] <- lengths