I am now performing transcript-level DE analysis using salmon-tximport-deseq2.
I have two questions: 1. what are the differentially expressed transcripts among conditions. 2. How isoforms of the same gene are differentially expressed among conditions.
- I simply input the salmon result by tximport with
txOut = TRUE, then perform DE analysis in deseq2 at the transcript-level.
- I will only pick some genes of interest so it would not be a global expression analysis. For example, a gene has transcript A and B, I hope to plot their expression levels against different conditions in one line chart or box plot. From my understanding, I should not use the normalized counts generated by deseq2 since they are only normalized for library size. Since I will compare/plot expressions of different isoforms in one plot, the reads should be normalized for both library size and transcript length right? Then TPM might be good to use? In that case, I can directly use the
abundanceof the tximport output?