Hello everybody, I ran a DE –RNAseq project by star-stringtie2- deseq2 pipline. The prepDE.py was used for generation of transcript matrix and gene matrix. Deseq2 were performed at both gene and transcript levels. At the gene level, 838 DE-genes were identified with -10< logFC< +10, it seems that this results are ok. But at the transcript level, just 112 DE-transcripts were identified with high logFC (-30<logFC < +30). Since, the transcripts are part of the genes; I don’t understand why the number of transcripts is less than the number of genes and why their logFC is higher? What is relationship between gene expression and transcript expression at deseq2? Is genes expression calculated based on the mean expression of their transcripts?