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Old 07-03-2015, 02:18 AM   #1
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Location: USA

Join Date: Jun 2015
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Default Cuffdiff output to GSEA

Hi all,
I'm a beginner in Bioinformatics and I'm now work on some RNA-seq results. I'm here looking for help in GSEA analysis and any advice will be appreciated

I went through the Tophat-cufflinks process and now I want to use the cuffdiff output to GSEA. It says that four types of files should be prepared for GSEA. For the gene set file, I used the MsigDB, and I used Fpkm_trackingToGct module from gene pattern to get gct file from my cuffdiff output. However, I'm not sure if there is any module or software I can use to get the cls and chip annotation file from the cuffdiff output files. Or if I need to make them by myself, the cls file might be easy but I'm not sure about the annotation file, and I'm not sure which chip file I should use from the broad ftp web site.

Thanks in advance for helping!
yaz1992 is offline   Reply With Quote
Old 08-25-2015, 02:31 PM   #2
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Location: Canada

Join Date: Aug 2015
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Hi Andrea,

Did you find a solution to this by any chance? I am currently stuck there as well, and I would really appreciate any guidance..

Thank you,
Yena is offline   Reply With Quote

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