**1.3k**wrote:

Hi all,

I am looking for a method to compare the significance of the expression difference of two different transcripts within a specific condition.

with that said, i will try to explain a bit more. We have a RNA-Seq experiment with three conditions. We are comparing each pair of conditions to find significant differentially regulated genes on gene (deseq2,cuffdiff) and transcript level (kallisto,cuffdiff,dexseq).

For some of the **transcripts** (isoforms of the same gene) we would like not only to know whether or not they are significant DE between the two conditions, but also if transcriptA is significantly higher/lower expressed than transcriptB.

About the data - we have 10 replicates for each of the three conditions.

For the first question I have done done the calculations with the mentioned tools. I am struggling to find a way to calculate the second problem. Is there a method to calculate such significances?

thanks for the help,

Assa