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:
http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise
And this FAQ can help with common troubleshooting:
http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq
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:
http://wiki.g2.bx.psu.edu/Support#Unexpected_scientific_result
Best wishes for your project,
Jen
Galaxy team
On 1/31/12 8:57 AM, 杨继文 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 <javascript:void(0);>". 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
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___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
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