We have 6 muscle types with 4 specific exons that look to be alternatively spliced are present in each muscle type.
We have paired-end Illumina RNASeq reads and we are working with a non-model organism with no reference genome. We have a working composite for a protein sequence that includes every exon we have found via cDNA.
As I understand it, Htseq-count finds the exons that reads overlap with and then groups counts based on the exon's gene ID in the GTF file. How do annotate my composite to show me the abundance at which theses 4 exons are expressed?