Question: Gene And Transcript Names From Cuffdiff
gravatar for 杨继文
6.1 years ago by
杨继文210 wrote:
Hi all, I am learning how to use Galaxy to analyze my RNA-Seq data. After running cuffdiff, one of the files I got is "transcript differential expression testing". In this file, I can see " gene_id" is something like "XLOC_000001". I am wondering how I can find the name of differentially expressed genes and transcripts. Can anyone help me?????? Thanks in advance. Jiwen
galaxy • 1.1k views
ADD COMMENTlink modified 6.1 years ago by Jennifer Hillman Jackson24k • written 6.1 years ago by 杨继文210
gravatar for Jennifer Hillman Jackson
6.1 years ago by
United States
Jennifer Hillman Jackson24k wrote:
Hello Jiwen, For Cufflinks to incorporate reference transcript and gene annotation (known gene names, as opposed to experimentally assigned labels), a correctly formatted reference GTF file will need to be used. This tutorial shows how this type of information is incorporated using the Cufflinks tool form: And this FAQ can help with common troubleshooting: Where to obtain a reference annotation GTF file can vary depending on the genome you are working with. The tool authors are a good resource to ask about potential sources. Contact information is in the "Example" RNA-seq" section of this wiki: Best wishes for your project, Jen Galaxy team -- Jennifer Jackson
ADD COMMENTlink written 6.1 years ago by Jennifer Hillman Jackson24k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 64 users visited in the last hour