Hi All

I am wondering if conceptually I can use the DESeq to test for differential
transcript expression compared to genes. In our case we have generated a
transcript model based on RNA-Seq and if we try to collapse those
transcripts to genes in order to do gene level differential expression many
exons are collapsed to give rise to artificial exons.


eg :


Transcript 1 :        ---------------------- (exon)
Transcript 2 :                        -----------------------------(exon )

Gene level :          -------------------------------------------- (exon)

Also another thing that comes to my mind if the effect of double counting
if I take the read counts at transcript level due to exon redundancy.

I would love to hear from your experience.

Thanks!
-Abhi

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