Why do some genes show no expression in STAR results across all samples, even though I can see mapped reads in the raw RNA-Seq data?

STAR gene expression quantification excludes reads that are mapped to multiple different genes. This can cause some genes to appear with zero expression in the final counts, even if mapped reads are present in the raw data. 

One common reason for this is gene overlap. These genes often have their exons entirely encompassed within other genes, and in such cases, STAR cannot assign reads to them because they are ambiguous. To check if a gene falls into this category, you can refer to the following lists: Stranded Counting Overlap Gene List: overlap.gene.stranded.tsv, and Strandless Counting Overlap Gene List: overlap.gene.strandless.tsv.