Hello,

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 )

thank you

The tximport paper discusses this point at length.

There are many considerations.