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Old 01-13-2014, 07:54 AM   #1
twotwo
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Location: Ohio

Join Date: May 2012
Posts: 40
Default Obtain the gene names for FPKM generated from cufflinks command

Hi,
I used the cufflinks command to generate the FPKM values. However, the genes.fpkm_tracking, which have the FPKM values, did not have the gene names. The following is my command.
cufflinks -o /mypath/cufflinks2 -g /mypath/hg19/hg19.gtf /mypath/tophat/accepted_hits.bam

I used UCSC hg19 as reference for both tophat and cufflinks.

And the following is part of the output:

tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus
CUFF.1 - - CUFF.1 - - chr1:11873-14409
CUFF.2 - - CUFF.2 - - chr1:14361-29370
NR_026820 - - NR_026820 - - chr1:34610-36081
NM_001005484 - - NM_001005484 - - chr1:69090-70008
CUFF.3 - - CUFF.3 - - chr1:323891-328581
CUFF.4 - - CUFF.4 - - chr1:134772-140566
NM_001005224 - - NM_001005224 - - chr1:367658-368597


The gene_id kept missing. Any comments? Thanks!
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