stringtie to assemble transcripts. I use
stringtie to make a
.gtf file, which outputs the following format:
... gene_id "X"; transcript_id "X"; FPKM "0.0111";.... The point is that each entry (transcript/exon) has a FPKM value associated with it (in the
I also use
stringtie to assemble transcripts into
t_data.ctab also provides FPKM values for each transcript.
My issue is that these FPKM values (for a specific transcript) do not match...has anyone else compared these values? Any idea why there's a difference? And which value I should trust?