I have mRNA count files with contains IDs like ENSG00000200494 (https://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000200494;r=20:16670641-16670742;t=ENST00000363624).
The ensembl website shows as noncoding part of RNAs. However, the file is supposed to contain rna-seq information related to only messenger RNA. I suspect there is something wrong during alignment with the reference transcriptome.
How do you think about it? Thank you.