Question about Cufflinks and reference annotations

[mhayes]

Hi,

I ran cufflinks with the -r option for performing reference annotation based transcript assembly. I used a reference GTF file downloaded from the UCSC genome browser (refFlat table). Here is an example of my output in the transcripts.gtf file:

chr1 Cufflinks transcript 1236828 1249909 1000 - . gene_id "CUFF.65"; transcript_id "CPSF3L"; FPKM "78.3979674437"; frac "0.481787"; conf_l
o "76.995976"; conf_hi "79.799959"; cov "1213.450041"; full_read_support "yes";
chr1 Cufflinks exon 1236828 1237167 1000 - . gene_id "CUFF.65"; transcript_id "CPSF3L"; exon_number "1"; FPKM "78.3979674437"; frac "0.481787
"; conf_lo "76.995976"; conf_hi "79.799959"; cov "1213.450041";
chr1 Cufflinks exon 1237261 1237390 1000 - . gene_id "CUFF.65"; transcript_id "CPSF3L"; exon_number "2"; FPKM "78.3979674437"; frac "0.481787
"; conf_lo "76.995976"; conf_hi "79.799959"; cov "1213.450041";
chr1 Cufflinks exon 1237469 1237611 1000 - . gene_id "CUFF.65"; transcript_id "CPSF3L"; exon_number "3"; FPKM "78.3979674437"; frac "0.481787
"; conf_lo "76.995976"; conf_hi "79.799959"; cov "1213.450041";

Cufflinks identifies the transcript as belonging to the CPSF3L gene. However, the gene id is listed as "CUFF.65".

Shouldn't the gene ID also be "CPSF3L"?

This is actually happening for the VAST majority of assembled transcripts; the program assigns the gene IDs "CUFF.x", but the transcript IDs are true gene identifiers.

Is this normal?

[hubery_Bio]

I have the same question with you! I am confused...
If you figured it out, please let me know, thank you.