cuffnorm got high fpkm TCONS but few read

Question

[xyp413826]

I use cufflinks to analyze RNA-seq data, when I finish the cuffnorm, I find very high fpkm in "isoforms.fpkm_table" or genes.fpkm_table, so I want to check if this is true, I use IGV to check the reads number, but I find the reads number are few, and I pick out the high fpkm TCONS sequence from the merged.transcript.gtf file, I find that all the TCONS sequence are very short! so I don't know happened about this.

[Asaf]

I didn't understand your question completely but what you say makes sense. Short genes with few reads should have higher fpkm than long genes with the same number of reads

[xyp413826]

Thanks, I am already figure out this question.

[Asaf]

I didn't understand your question completely but what you say makes sense. Short genes with few reads should have higher fpkm than long genes with the same number of reads