I'm using tximport before before running DESeq2.
Tximport can summarize counts to gene-level by default or we can avoid gene-level summarization by setting txOut=TRUE using the original transcript level estimation.
Can you please tell me what's the correct way for the analysis with DESeq2?
I noticed that there is a huge difference when I use the txOut argument and when I don't
here is the code:
txi.salmon <- tximport(files, type="salmon", tx2gene=tx2gene, ignoreAfterBar=TRUE,txOut = TRUE )