Hi, So I'm currently analyzing some RNA-seq datasets and wanted to get expression at the gene level. So I got raw counts with featureCounts and then got normalized counts using DESeq2.
My question is, I have huge genes with very high introns. I'm afraid the normalization is taking into account the whole gene length, so expression in exons of genes with huge introns would be underrated. I believe DESeq-2 normalizes depending on the total on reads but I don't know if the fact that I have huge introns might be confounding in oter parts of the analysis. Maybe I can perform the analyses at the exon level and then somehow combine the counts per gene? Don't know if that's crazy
Any thoughts? Thanks for any help