What is the Sleuth intercept and how can Sleuth be used when you have >2 treatment types?
1
1
Entering edit mode
4.8 years ago
james.lloyd ▴ 100

Hello Internet,

So I have an issue where I have more than one treatment. Treatment A, Treatment B, Treatment C and Treatment D (for example). I want to use kallisto or salmon to quant the transcripts and then use Sleuth to find differential transcripts. But I do not understand the commands very well.

When you run sleuth, you might get

models(so): coefficients: (Intercept) condTreatmentB condTreatmentC condTreatmentD

But what is (Intercept) and where is condition A? When I want to do differential testing between Treatment A and Treatment B, how do I do it? And then how do I change it to Treatment A and Treatment C? Or change it to Treatment B and Treatment C?

Please help me, you are my only hope.

Best, James

RNA-Seq sleuth kallisto salmon DTE • 2.2k views
ADD COMMENT
0
Entering edit mode

Did you get it?

I'm now in the same situation.

Thanks!!

LucĂ­a

ADD REPLY
0
Entering edit mode

Do you have an update you could share?

ADD REPLY
0
Entering edit mode
ADD COMMENT

Login before adding your answer.

Traffic: 1998 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6