Fpkm Values Of Cumerge Transcripts Are Low

Question

[gireeshkbogu]

Hi,

I merged two transcripts using cuffmerge that are de novo assembled by cufflinks. The resulting cuffmerge-transcript.gtf has very low FPKM values compared to cufflinks-transcripts.gtf files. More importantly the cuffmerge-transcripts.gtf file FPKM values are in between 0 and 1 range, where as cufflinks-transcripts 0 to 160,000 range. I used the following commands ...

Does any one know why cuffmerge is producing weird FPKM scores ?

cufflinks -o cufflinks_rep1 tophat_h1hesc_rep2/accepted_hits.bam
cufflinks -o cufflinks_rep2 tophat_h1hesc_rep2/accepted_hits.bam

assemblies.txt:
cufflinks_rep1/transcripts.gtf
cufflinks_rep2/transcripts.gtf

cuffmerge -s hg19.fa assemblies.txt