Obtain the gene names for FPKM generated from cufflinks command

twotwo · 01-13-2014, 07:54 AM

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!

Zapages · 01-13-2014, 06:14 PM

hmm maybe loading the files into NCBI IGV and seeing what matches up based on the chromosome location. The chromosome location are indicated.

Steps:

1) Load the your UCSC hg19 into NCBI IGV
2) Load your GTF files and BAM hits files to see the results.

I hope this helps a bit.

rboettcher · 01-14-2014, 01:23 AM

Try bedtools intersect with your Cufflinks GTF and the GTF you used as reference annotation to see if there is any known annotation in the regions identified by Cufflinks (which should not be the case).

FYI: -g means that Cufflinks will perform a RABT assembly of novel transcripts, in case you only want quantification of known genes use -G.

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
tophat/cufflinks no gene names or annotations showing up	sagarc88	Bioinformatics	2	10-05-2015 12:27 PM
A post-doc and the case of the disappearing gene names (in Cufflinks/cuffdiff)	amcloon	RNA Sequencing	10	07-12-2013 12:01 PM
converting UCSC gene names to Hugo Symbol names	efoss	Bioinformatics	2	07-16-2011 01:41 PM
Obtain Spliced Read Names/Mapping with TopHat??	mendl7	Bioinformatics	7	09-20-2010 11:53 AM
inconsistent gene names in genes.expr - Cufflinks	Boel	Bioinformatics	2	04-14-2010 06:16 AM

01-13-2014, 07:54 AM	#1
twotwo Member Location: Ohio Join Date: May 2012 Posts: 40	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!

01-13-2014, 06:14 PM	#2
Zapages Member Location: NJ Join Date: Oct 2012 Posts: 97	hmm maybe loading the files into NCBI IGV and seeing what matches up based on the chromosome location. The chromosome location are indicated. Steps: 1) Load the your UCSC hg19 into NCBI IGV 2) Load your GTF files and BAM hits files to see the results. I hope this helps a bit.

01-14-2014, 01:23 AM	#3
rboettcher Member Location: Berlin Join Date: Oct 2010 Posts: 71	Try bedtools intersect with your Cufflinks GTF and the GTF you used as reference annotation to see if there is any known annotation in the regions identified by Cufflinks (which should not be the case). FYI: -g means that Cufflinks will perform a RABT assembly of novel transcripts, in case you only want quantification of known genes use -G.