question about cufflinks

[caswater]

Just got result from cufflinks but not quite understand the output genes.fpkm_tracking:

I used this command:

cufflinks -o Result -p 4 -g $GTF -b $RefGenome -u $file

I then wish to check the estimated genes, but found only around 6000 genes (with known gene symbols) were reported in genes.fpkm_tracking, while the remaining are all with ids like CUFF.XXX, see below...

So I was just wondering how I could know the expression of all ~20000 genes in the RTF annotation files, and CUFF.xxx corresponds to which gene?

Thanks

tracking_id	class_code	nearest_ref_id	gene_id	gene_short_name	tss_id	locus	length	coverage	FPKM	FPKM_conf_lo	FPKM_conf_hi	FPKM_status
OR4F5	-	-	OR4F5	-	-	chr1:69090-70008	-	-	0	0	0	OK
CUFF.4	-	-	CUFF.4	-	-	chr1:109920-110286	-	-	1.57124	0.830549	2.31193	OK
FAM138A	-	-	FAM138A	-	-	chr1:34610-36081	-	-	0	0	0	OK
CUFF.6	-	-	CUFF.6	-	-	chr1:126628-127545	-	-	0.207493	0.0923964	0.322589	OK
CUFF.5	-	-	CUFF.5	-	-	chr1:125397-125894	-	-	0.804427	0.435331	1.17352	OK
CUFF.8	-	-	CUFF.8	-	-	chr1:167776-168206	-	-	1.66698	1.04788	2.28608	OK
CUFF.10	-	-	CUFF.10	-	-	chr1:163967-164488	-	-	0.425551	0.168934	0.682169	OK
CUFF.9	-	-	CUFF.9	-	-	chr1:169060-169232	-	-	1225.18	702.763	1747.6	OK
CUFF.11	-	-	CUFF.11	-	-	chr1:227422-227796	-	-	7.54204	5.96942	9.11467	OK
CUFF.12	-	-	CUFF.12	-	-	chr1:233147-233979	-	-	0.292227	0.146113	0.43834	OK
CUFF.13	-	-	CUFF.13	-	-	chr1:234725-235592	-	-	0.379276	0.217552	0.540999	OK
CUFF.14	-	-	CUFF.14	-	-	chr1:234090-234614	-	-	0.612381	0.306191	0.918572	OK