Question: How to covnvert gene id to gene names
0
gravatar for shikhascorpio4
6 months ago by
shikhascorpio40 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

ADD COMMENTlink modified 6 months ago by Jennifer Hillman Jackson25k • written 6 months ago by shikhascorpio40
0
gravatar for Jennifer Hillman Jackson
6 months ago by
United States
Jennifer Hillman Jackson25k 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 COMMENTlink written 6 months ago by Jennifer Hillman Jackson25k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 88 users visited in the last hour