I have sequencing data reflecting the amount of nascent mRNA and I have from the same biological samples data reflecting the polyA fraction. both for two conditions (treated and unteated). I plan to do differential gene expression analysis on the nascent RNA-seq (to get an idea of differential transcription). In a next step I would like to test the polyA fraction sequencing data if they differ from the nascent RNAseq data, which could be indicative of differential decay/stability. To this end I do not want to test the hypothesis that the log2FC(polyA gene) != 0 but log2FC(polyA gene) != log2FC(nascent gene).
I did find the lfcThreshold, altHypothesis options. But I can not provide a lfcThreshold for each gene individually. Furthermore I do not have an unequal altHypothesis.
I thought about doing it with contrasts but could not figure out how. If I would do something like '~ nascent + condition' I would fake additional replicas.
Any idea how to do this properly is highly welcomed. Thank you very much in advance.