SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics

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

Reply
 
Thread Tools
Old 01-13-2014, 07:54 AM   #1
twotwo
Member
 
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!
twotwo is offline   Reply With Quote
Old 01-13-2014, 06:14 PM   #2
Zapages
Member
 
Location: NJ

Join Date: Oct 2012
Posts: 97
Default

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.
Zapages is offline   Reply With Quote
Old 01-14-2014, 01:23 AM   #3
rboettcher
Member
 
Location: Berlin

Join Date: Oct 2010
Posts: 71
Default

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.
rboettcher is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 07:05 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO