Question: tximport and txOut
0
4 weeks ago by
Merlin 10
Italy
Merlin 10 wrote:

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

deseq2 tximport • 72 views
modified 4 weeks ago by Michael Love23k • written 4 weeks ago by Merlin 10
1
4 weeks ago by
Michael Love23k
United States
Michael Love23k wrote:

The tximport paper discusses this point at length.

There are many considerations.

Which one is the paper?

probably if I want to do differential gene expression I can just use the default txOut= FALSE while if I want to do analysis at trascript level for the screening of different isoforms I need of txOut= TRUE

thanks