Question: Gene And Transcript Names From Cuffdiff
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gravatar for 杨继文
6.6 years ago by
杨继文210
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 • 1.3k views
ADD COMMENTlink modified 6.6 years ago by Jennifer Hillman Jackson25k • written 6.6 years ago by 杨继文210
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gravatar for Jennifer Hillman Jackson
6.6 years ago by
United States
Jennifer Hillman Jackson25k 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: 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 -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support
ADD COMMENTlink written 6.6 years ago by Jennifer Hillman Jackson25k
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