==> transcripts.gtf.refmap <==
ref_gene_id	ref_id	class_code	cuff_id_list
ODF3	ENST00000342593	c	CUFF.3002651|CUFF.3002651.1
ODF3	ENST00000325113	c	CUFF.3002653|CUFF.3002653.1,CUFF.3002651|CUFF.3002651.1
RIC8A	ENST00000325207	c	CUFF.3002675|CUFF.3002675.1,CUFF.3002667|CUFF.3002667.1,CUFF.3002665|CUFF.3002665.1
NLRP6	ENST00000312165	c	CUFF.3002715|CUFF.3002715.1
ATHL1	ENST00000474221	c	CUFF.3002721|CUFF.3002721.1
ATHL1	ENST00000312105	c	CUFF.3002721|CUFF.3002721.1
ATHL1	ENST00000409655	c	CUFF.3002721|CUFF.3002721.1
ATHL1	ENST00000482937	c	CUFF.3002721|CUFF.3002721.1
ATHL1	ENST00000397660	c	CUFF.3002721|CUFF.3002721.1

==> genes.fpkm_tracking <==
tracking_id	class_code	nearest_ref_id	gene_short_name	tss_id	locus	1_FPKM	1_conf_lo	1_conf_hi	2_FPKM	2_conf_lo	2_conf_hi
XLOC_000001	-	-	ODF3	-	chr11:196838-196888	60.048	44.5499	75.5461	603.211	554.091	652.332
XLOC_000002	-	-	RIC8A	-	chr11:208522-208573	70.9297	54.0858	87.7737	501.335	456.554	546.116
XLOC_000003	-	-	PSMD13	-	chr11:251566-251616	36.4577	24.3817	48.5338	0	0	0
XLOC_000004	-	-	NLRP6	-	chr11:281128-281178	57.9034	42.6846	73.1223	129.69	106.914	152.467
XLOC_000005	-	-	ATHL1	-	chr11:290034-290084	45.036	31.6142	58.4578	211.124	182.064	240.184
XLOC_000006	-	-	IFITM2	-	chr11:309219-309459	1.48406	0	3.9205	0	0	0
XLOC_000007	-	-	IFITM1	-	chr11:314236-314286	0	0	0	120.642	98.6748	142.61
XLOC_000008	-	-	B4GALNT4	-	chr11:369866-369916	155.507	130.567	180.447	102.546	82.2929	122.799
XLOC_000009	-	-	PKP3	-	chr11:403489-403652	3.56827	0	7.35334	19.2292	10.4507	28.0078

==> /cccbstore-rc/projects/db/genomes/human/hg18/gtf/Hs_hg18_Ens_cuff.gtf <==
chr11	pseudogene	exon	86648	87586	.	-	.	 gene_id "ENSG00000224777"; transcript_id "ENST00000424047"; exon_number "1"; gene_name "OR4F2P"; transcript_name "OR4F2P-001";
chr11	protein_coding	exon	129059	129388	.	-	.	 gene_id "ENSG00000230724"; transcript_id "ENST00000382784"; exon_number "1"; gene_name "AC069287.3"; transcript_name "AC069287.3-201";
chr11	protein_coding	exon	127925	128376	.	-	.	 gene_id "ENSG00000230724"; transcript_id "ENST00000382784"; exon_number "2"; gene_name "AC069287.3"; transcript_name "AC069287.3-201";
chr11	protein_coding	exon	130932	131297	.	-	.	 gene_id "ENSG00000230724"; transcript_id "ENST00000457006"; exon_number "1"; gene_name "AC069287.3"; transcript_name "AC069287.3-204";
chr11	protein_coding	exon	128959	129752	.	-	.	 gene_id "ENSG00000230724"; transcript_id "ENST00000457006"; exon_number "2"; gene_name "AC069287.3"; transcript_name "AC069287.3-204";
chr11	protein_coding	exon	138955	139099	.	-	.	 gene_id "ENSG00000230724"; transcript_id "ENST00000435244"; exon_number "1"; gene_name "AC069287.3"; transcript_name "AC069287.3-203";
chr11	protein_coding	exon	138046	138111	.	-	.	 gene_id "ENSG00000230724"; transcript_id "ENST00000435244"; exon_number "2"; gene_name "AC069287.3"; transcript_name "AC069287.3-203";
chr11	protein_coding	exon	133587	133778	.	-	.	 gene_id "ENSG00000230724"; transcript_id "ENST00000435244"; exon_number "3"; gene_name "AC069287.3"; transcript_name "AC069287.3-203";
chr11	protein_coding	exon	131466	131524	.	-	.	 gene_id "ENSG00000230724"; transcript_id "ENST00000435244"; exon_number "4"; gene_name "AC069287.3"; transcript_name "AC069287.3-203";
chr11	protein_coding	exon	129735	131373	.	-	.	 gene_id "ENSG00000230724"; transcript_id "ENST00000435244"; exon_number "5"; gene_name "AC069287.3"; transcript_name "AC069287.3-203";