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

Did you get it?

I'm now in the same situation.

Thanks!!

LucĂa

Do you have an update you could share?