Question: Fpkm Values Of Cumerge Transcripts Are Low
gravatar for gireeshkbogu
7.5 years ago by
gireeshkbogu0 wrote:


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


cuffmerge -s hg19.fa assemblies.txt
cufflinks cuffmerge rna-seq • 2.1k views
ADD COMMENTlink written 7.5 years ago by gireeshkbogu0
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