So basically I want to investigate whether there is a switch in isoform preference between condition 1 and condition 2. My idea was to conduct differential expression analysis on the data. If isoformA have decreased differential expression and isoformB have increased differential expression from condition 1 to condition 2, there is a shift in isoform preference.
Fortunately, I have rsem data so I just need a tool that does what I want which is also my issue. From doing my own investigation rsem tends to be paired with EBseq for analysis, so I looked up the manual from EBseq. Based on the manual, the output of EBseq only informs whether an isoform is differentially expressed or equivalently expressed based on your FDR. I need a tool that gives some fold change.
Tools like DESeq2 will give me the results in the form I want but according to various posts, using isoform counts will violate the underlying assumptions of these tool.
Is there any tool that is made for isoform data and produces output that i want or is it acceptable to adapt DESeq2 to my purposes?