I have analysed an mRNA sequencing dataset (~30 million reads for each of the two biological replicates per sample for two samples, generated from poly-A enrichment library) using STAR-Featurecounts-EdgeR protocol. I see 110 tRNA genes are differentially expressed in my mutant compared to control (DE genes defined as log2FC >1.5 or log2FC <-1.5 along with FDR <0.05).
Now, since tRNA transcripts are not poly adenylated (unless marked for degradation), they are not supposed to be enriched in my mRNA sequencing library. But if those tRNA molecules are coming into my library just due to random chance and their relative abundance, is it correct to analyse differential expression for them? The read counts for some of them are very low (0-50) but most of them are > 50.
I would like to know if 1. anybody has seen tRNA reads in mRNA sequencing experiment done with poly-A enrichment library and 2. if yes, then it is correct to compare their expression levels?
Thank you for your help!