Just a thought, I notice that in the ensemble.gtf file the protein ids are listed as follows:

chr11	protein_coding	CDS	129060	129388	.	-	0	 gene_id "ENSG00000230724"; transcript_id "ENST00000382784"; exon_number "1"; gene_name "AC069287.3"; transcript_name "AC069287.3-201"; protein_id "ENSP00000372234"
Is the p_id problem in cufflinks because the ensemble.gtf file uses the word protein_id and not p_id???


Cheers
David



__________________________________
Dr David A. Matthews

Senior Lecturer in Virology
Room E49
Department of Cellular and Molecular Medicine,
School of Medical Sciences
University Walk,
University of Bristol
Bristol.
BS8 1TD
U.K.

Tel. +44 117 3312058