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Question: gene id missing
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gravatar for mis
3.3 years ago by
mis • 0
United States
mis • 0 wrote:

Hi ,

I run the tophat, cufflinks, cuffmerge and cuffdiff on a human data set. I used h19 as reference genome. However I am not able to get the gene id in my output. I used also the gene annotation from chromosome 19 and still didn't get it. I am new in this, so i would really appreciate the help.  

 

Thank you
cufflinks • 1.2k views
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modified 3.3 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.3 years ago by mis • 0

But you get the ENSEMBL ID, isn't it?

ADD REPLY • link written 3.3 years ago by Bjoern Gruening ♦ 5.1k

No, I don't. I am getting some CUFF numbers from cufflinks but no information on gene name.

ADD REPLY • link written 3.3 years ago by mis • 0
0
gravatar for Jennifer Hillman Jackson
3.3 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Double check your reference annotation file (GTF or GFF3). Make sure it has the attributes tss_id, p_id, and gene_name, for full statistics and incorporation of the annotation. 

Also make certain that you use this at the Cuffmerge step, when combining the Cufflinks GTF datasets. Any transcripts not in the Cuffmerge results will be ignored when later running Cuffdiff.

The website for the Tuxedo pipeline has details about reference data and attributes. This is a good place to start: 
http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/index.html#cuffdiff-input-files

I wasn't sure if this was a continuation of a previous conversation/Q&A, so apologies if this is duplicated info.

Best, Jen, Galaxy team
ADD COMMENT • link modified 3.3 years ago • written 3.3 years ago by Jennifer Hillman Jackson ♦ 25k
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