I have aligned RNA-Seq data from human samples to GRCh37. The flattened file has also been created using the same database using the dexseq_prepare_annotation.py and the counts have been generated using the dexseq_counts.py script. However, the total number of exon for most of the genes are greater than what has been reported in literature. e.g. SNCA, which is reported to have 5 exons shows 26 exons in the analysis and in the flattened file. I have previously worked with the mouse genome using GRCh38 but have not had any issue. What could be going wrong?
Thanks in advance for your suggestions,