this is an example of my CuffDiff gene fpkm tracking file.

tracking_id class_code nearest_ref_id gene_short_name tss_id locus q1_FPKM q1_conf_lo q1_conf_hi q2_FPKM q2_conf_lo q2_conf_hi XLOC_000001 - - MT-ND5 - chrM:0-16571 12484.2 12260.8 12707.7 11447 11233.1 11661 XLOC_000002 - - USP14 TSS1,TSS2,TSS3 chr18:148586-236453 16.7235 9.41244 24.0346 19.437 11.7368 27.1371 XLOC_000003 - - SMCHD1 TSS10,TSS11,TSS12,TSS4,TSS5,TSS6,TSS7,TSS8,TSS9 chr18:2719322-2728540 28.2493 17.5093 38.9892 27.2263 16.6263 37.8262 XLOC_000004 - - EMILIN2 TSS13,TSS14 chr18:2880607-2882469 3.98118 0 7.99721 4.62875 0.278519 8.97899

I this is normal, how can I find the class code of transcript listed in the CuffDiff gene expression file?

Hi Samuele, Without seeing your history, it's difficult to say for certain what your problem is. However, I'd guess that the GTF file that you're providing to Cuffdiff does not have the p_id attribute. You can produce a GTF file with both tss_id and p_id attributes by running Cuffcompare and using sequence data. Thanks, J.