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Question: How to covnvert gene id to gene names
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gravatar for shikhascorpio4
7 months ago by
shikhascorpio4 • 0
shikhascorpio4 • 0 wrote:

Hi, I have been using Tophat, cufflink, cuffmerge and cuffdiff to analyse RNA seq data. I have been getting this test_id gene_id gene XLOC_000041 XLOC_000041 gene10113-v1.0-hybrid Is there a way that i can convert them into gene names. I have searched ensemble plants (was planning to use biomart ) too but my genus does not exist there.

Thanks in advance for your help and suggestions
rna-seq annotation gtf cufflinks gene • 407 views
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modified 7 months ago by Jennifer Hillman Jackson ♦ 25k • written 7 months ago by shikhascorpio4 • 0
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gravatar for Jennifer Hillman Jackson
7 months 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.

Variations of this question have been asked many times before -- so please review the prior Q&A for more details. Examples: https://biostar.usegalaxy.org/p/24566/, https://biostar.usegalaxy.org/p/21827/, https://biostar.usegalaxy.org/p/19911/

Current Galaxy RNA-seq tutorials: https://galaxyproject.org/learn/

Thanks! Jen, Galaxy team
ADD COMMENT • link written 7 months ago by Jennifer Hillman Jackson ♦ 25k
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