Exon/junctions count

[Song Rhondda]

Hi, 

I'm trying to get the count number of exon and junction reads per gene, not just the overall count number per gene. For example, in the gtf annotation file, every gene_id includes more than 1 exon_id. Can we just count the number of exon group by gene_id and exon_id?  by using --quantMode GeneCounts, it only counts per gene. I want to have count per exon. Any suggestions? and is there is a way to count junctions per gene?

thanks for your help.

[Alexander Dobin]

Hi,

counting reads per exons is not trivial.

Typically, exons belong to many overlapping transcripts, so the same exon repeats multiple times in the GTF file.

Also, you need to deal with the overlapping exons.

If you can create a set of non-overlapping "super-exons", you can do the counting on them instead of genes.