Do I need to only keep exon in gene GTF when I run Cuffdiff?

Question

[bxia]

Do I need to only keep exon in gene GTF when I run Cuffdiff?

if I don't remove CDS etc,., will it cause problem?

Answer 1

[Petr Ponomarenko]

I do not remember having problems with this. I believe I tried with cds, mRNA and genes alongside exons. Do you get different results with and without CDS in GTF?

[bxia]

I am completely not sure, I just find some command and realize people use exon only GTF to map.

Haven't try that yet.