Hi,
I used cufflinks with an annotation (-g option). In the isoforms.fpkm file and the transcripts.gtf file a particular isoform of a gene is present with a high FPKM value, the gene_id being ENSG00000169083.11 according to the annotation. However, cufflinks has assigned its own gene_id CUFF.19478 instead and this is how it looks like in the transcripts.gtf file.
"chrX Cufflinks transcript 66788731 66944130 1000 + . gene_id "CUFF.19748"; transcript_id "ENST00000396043.2"; FPKM "15.2953330876"; frac "0.282033"; conf_lo "12.637576"; conf_hi "17.953090"; cov "14.343481"; full_read_support "yes";"
Can someone please explain why this happens and a possible solution? I want to find known genes and this gives me trouble.
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