and what if use GFT ?
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How To Stated Out Name Of Gene In Cufflink Genes.Fpkm_Tracking
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
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Michael Dondrup
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smagikern •
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smagikern •
1 answer
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.
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Michael Dondrup
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/.
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