I am reading the literature "Link" and I have seen terminologies which are the following:
Differential transcript expression (DTE) refers to change in one of the isoforms.
Differential gene expression (DGE) refers to change in overall gene expression (i.e. expression as the sum of the expression of the two isoforms).
Differential transcript usage (DTU) refers to change in relative expression between the two isoform.
Gene differential expression (GDE) refers to change in expression along the red line.
Now I want to know which isoform of some specific gene (lets say TGF-beta) is highly expressed and which one in less expressed in certain tissue. According to my understanding I need to do DTE analysis. if so what workflow should i use.
Thanks
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DEXseq
Isn't DEXseq for DTU ?
DTU implies DTE, as I understand.
How ? Can you please explain it. I could not find any good source to understand it?
Salmon + fishpond is my personally recommended workflow for DTE and DTU. Make sure to add inferential replicates with Salmon for more accurate results.
Currently I am using Salmon and DRIMseq. But I think I am unable to understand the output. I created the Table]1 . Please tell me if i am write or wrong. Here geneID is DTE and txID are DTU? and does the fishpond will produce similar outpuy???