Dear All, i have completed an RNA seq differential expression pipeline and am currently attempting to analyse my results. I had been using the differential expression testing for transcripts output to compare expression between two conditions. Unfortunately in these outputs several entries (relating to different transcript variants) can be found for each gene. I was going to look at these individually but from the CuffDiff output there seems to be no way to know the difference between these transcripts and as a result which variant is of higher biological importance in terms of expression of a fully functional protein. The only difference i can see in the cuffdiff output between different transcript variants appears to be the test_id, i thought this was an arbitrary number which cuffdiff applies to each transcript and as a result can't be used to tell how these transcript variants differ.
I was thinking about looking at the differential expression testing for genes, i assume this output simply groups the different transcript variants based on the gene they originate from. I am not sure that this is the best way to go though, as proteins are produced from transcripts not genes.
Any advice on how to proceed would be greatly appreciated!
RH
I was thinking about looking at the differential expression testing for genes, i assume this output simply groups the different transcript variants based on the gene they originate from. I am not sure that this is the best way to go though, as proteins are produced from transcripts not genes.
Any advice on how to proceed would be greatly appreciated!
RH