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
D.A.Matthews(a)bristol.ac.uk