I am interested in counting the number of reads that span splice junctions. Therefore, I set the options GTF.featureType = "transcript", useMetaFeatures = FALSE, and juncCounts = TRUE. However, the resulting counts matrix has row names like ENSG00000223972.5_1 and many of them are duplicated. What combination of parameters should be used to make the row names be transcript identifiers? Also, the counts_junction data frame has no feature identifiers, just NAs in the first two columns with these settings.
Also, the annotation element of the result is a data frame with a column named GeneID. This isn't the a suitable column name if GTF.attrType is not "gene_id".