I am working with a bulk RNA-seq dataset with a very high % of intronic counts (40-60% of mapped reads), which I believe come from pre-mRNA fraction and maybe to a lesser extent intron-retention in some transcripts. I am a bit concerned as the exonic counts for some sample are only about 1 million mapped reads. The tools that I am analyzing the data with only consider exonic reads for calculating gene expression. I am wondering how accurate would my gene expression be. Although the read depth that I sequenced the samples were good for my purpose (~15-20 million reads/sample), the low mapped % in exonic regions makes me a bit concerned. As I understand the genes with high expression would still be OK in this case correct? It is only the ones with low expression levels that's problematic. Any insights would be highly appreciated.