Question: What does 'frac' mean in cufflinks output transcripts.gtf
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gravatar for Jackie
15 months ago by
Jackie60
United States
Jackie60 wrote:

In Cufflinks output transcripts.gtf, there is a field called 'frac'. What does that mean?

chr1 Cufflinks transcript 18957500 19062632 361 + . gene_id "PAX7"; transcript_id "NM_002584.2"; FPKM "218.4530519923"; frac "0.219171"; conf_lo "200.428676"; conf_hi "236.477428"; cov "91.198450";

chr1 Cufflinks transcript 18957500 19062632 1000 + . gene_id "PAX7"; transcript_id "NM_013945.2"; FPKM "604.2821634224"; frac "0.604541"; conf_lo "570.899379"; conf_hi "637.664948"; cov "252.272037";

chr1 Cufflinks transcript 18957500 19075360 103 + . gene_id "PAX7"; transcript_id "NM_001135254.1"; FPKM "62.7113530728"; frac "0.176288"; conf_lo "57.679493"; conf_hi "67.743214"; cov "26.180354";

transcripts.gtf lists the isoform-level FPKM, if I need to calcualte gene-level FPKM, how to use the information in transcripts.gtf?

Thanks,

frac cufflinkts fpkm • 497 views
ADD COMMENTlink modified 15 months ago • written 15 months ago by Jackie60

Is there a "genes.fpkm_tracking" file in your result? Gene level FPKM should be there.

also, based on the manual, you should ignore the frac field.

ADD REPLYlink modified 15 months ago • written 15 months ago by shunyip160
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