How To Stated Out Name Of Gene In Cufflink Genes.Fpkm_Tracking

Question

[smagikern]

I have

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
CUFF.2    -    -    CUFF.2    -    -    chr1:793387-794366    -    -    0.716182    0.333366    1.099    OK
CUFF.3    -    -    CUFF.3    -    -    chr1:909711-911248    -    -    0.741928    0.432522    1.05133    OK
CUFF.4    -    -    CUFF.4    -    -    chr1:896634-901818    -    -    2.00204    1.58358    2.42049    OK
CUFF.5    -    -    CUFF.5    -    -    chr1:900198-902347    -    -    1.06585    0.764552    1.36714    OK
CUFF.6    -    -    CUFF.6    -    -    chr1:934344-935467    -    -    7.16842    4.38261    9.95423    OK
CUFF.7    -    -    CUFF.7    -    -    chr1:934556-934759    -    -    10.8507    4.47829    17.2231    OK

I need something like

TP53    -    -    TP53    -    -    chr1:793387-794366    -    -    0.716182    0.333366    1.099    OK
ACF    -    -    ACF    -    -    chr1:909711-911248    -    -    0.741928    0.432522    1.05133    OK
JKUI    -    -    JKUI    -    -    chr1:896634-901818    -    -    2.00204    1.58358    2.42049    OK
AKL    -    -    AKL    -    -    chr1:900198-902347    -    -    1.06585    0.764552    1.36714    OK
HJR    -            HJR    -    -    chr1:934344-935467    -    -    7.16842    4.38261    9.95423    OK
JKK    -    -    JKK    -    -    chr1:934556-934759    -    -    10.8507    4.47829    17.2231    OK

CUFF.3 -> TP53

Answer 1

[Michael]

Afaik, these names are the gene IDs that are used in the genome annotation GFF file. If you prepare or download a GFF file with the correct genome annotation and use this for the cufflinks run, the IDs in the GFF will be used.

[smagikern]

and what if use GFT ?

[Michael]

You mean GTF? Haven't tried that, I have used only files in GFF3 format. What's the organism, for most annotated genomes, GFF3 format annotation should be easy to obtain from the ncbi ftp server: ftp://ftp.ncbi.nih.gov/genomes/.