Question: How To Stated Out Name Of Gene In Cufflink Genes.Fpkm_Tracking
0
gravatar for smagikern
4.8 years ago by
smagikern0
smagikern0 wrote:

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

genes • 2.0k views
ADD COMMENTlink modified 4.8 years ago by Michael Dondrup44k • written 4.8 years ago by smagikern0
2
gravatar for Michael Dondrup
4.8 years ago by
Bergen, Norway
Michael Dondrup44k wrote:

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.

ADD COMMENTlink written 4.8 years ago by Michael Dondrup44k

and what if use GFT ?

ADD REPLYlink written 4.8 years ago by smagikern0

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/.

ADD REPLYlink written 4.8 years ago by Michael Dondrup44k
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