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???
__________________________________ 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