Question: tximport and txOut
gravatar for Merlin
12 weeks ago by
Merlin 10
Merlin 10 wrote:


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 • 96 views
ADD COMMENTlink modified 12 weeks ago by Michael Love24k • written 12 weeks ago by Merlin 10
Answer: tximport and txOut
gravatar for Michael Love
12 weeks ago by
Michael Love24k
United States
Michael Love24k wrote:

The tximport paper discusses this point at length.

There are many considerations.

ADD COMMENTlink written 12 weeks ago by Michael Love24k

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


ADD REPLYlink written 12 weeks ago by Merlin 10
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