Question: tximport and txOut
0
gravatar for Merlin
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
ADD COMMENTlink modified 4 weeks ago by Michael Love23k • written 4 weeks ago by Merlin 10
Answer: tximport and txOut
1
gravatar for Michael Love
4 weeks ago by
Michael Love23k
United States
Michael Love23k wrote:

The tximport paper discusses this point at length.

There are many considerations.

ADD COMMENTlink written 4 weeks ago by Michael Love23k

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

ADD REPLYlink written 4 weeks ago by Merlin 10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 117 users visited in the last hour