Hi,

I am trying to understand the counting done by HTseq using Ensemble GTF file. Here is an example:

GeneA_isoform1: Exon1              Exon2    Exon3
GeneA_isoform2: Exon1                              Exon3
GeneA_isoform3:Exon1                                               Exon4

When counting at gene level, I assume the reads that fall on all exons (Exon1, Exon2, Exon3 and Exon4) are all summed up for GeneA.

When counting at isoform level,

GeneA_isoform1 - is it sum of exons from Exon1, Exon2 and Exon3 (or) just reads that map to Exon2?
GeneA_isoform2 - is it sum of Exon1 and Exon3 (or) no counts because its exons are common with isoform1 and isoform3?
GeneA_isoform3 - sum of Exon1 and Exon4 (or) only Exon4?

Thank you very much for the clarification.

Best Regards,
Nirmala




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