Question: What does 'frac' mean in cufflinks output transcripts.gtf
0
gravatar for Jackie
7 months ago by
Jackie40
United States
Jackie40 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 • 242 views
ADD COMMENTlink modified 7 months ago • written 7 months ago by Jackie40

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 7 months ago • written 7 months ago by shunyip140
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1209 users visited in the last hour