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,
On 1/31/12 8:57 AM, 杨继文 wrote:
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
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.
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