Hi,

  I want to obtain read counts at the exon level using featureCounts. I run Rsubread and use these options:

annot.ext="/home/inah/RefGTF/GRCh38/annotation/Homo_sapiens.GRCh38.85.gtf",
isGTFAnnotationFile=TRUE,
GTF.featureType="exon",  GTF.attrType="exon_id",  useMetaFeatures=FALSE

The resulting count matrix has 1,182,163 rows but only 678,276 unique row identifiers, so there are multiple rows for the same exon-id.

Of course when I set useMetaFeatures=TRUE, then the resulting count matrix has 678,276 rows all with unique identifiers.

Sorry for the ignorant question, but why do I have so many more "exons" than "exon-ids"?

Thanks, Ina