My experience with single-cell RNA-seq shows that the inclusion of intronic reads improves the sensitivity for several genes of interest, which otherwise have zero expression when only exonic reads are considered. While single-cell sequencing quantifiers now often have options to count intronic reads, the bulk alignment-based quantifiers (let's say RSEM or Cufflinks) don't seem to me to count intronic reads by reading their manuals.
Currently the only way I can think of to count exon+intron reads in bulk RNA-seq data is by using
htseq-count with the
-t transcript option, but am I right in this? In addition, are there other ways I can use? Note that I only need gene-level counts.
Thanks for your answer in advance!