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Old 05-01-2011, 04:42 AM   #2
honey
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Location: Pittsburgh

Join Date: Feb 2010
Posts: 151
Default cufflink output

Huijuan,

You have very good understanding of RNA-seq work flow. I agree that Cufflinks/ Cuffdiff documentation and authors are always silent on this subject. This same question is being asked several time here in this forum and in other such discussion forums. I am now feeling that it was just one publication/s and no further assistance to fellow researcher. I used to use this work flow you are using. I am not an expert but can suggest that you look for unique Ids from differential expression files in combined GTF files. For gene level I have taken FPKM values and taken average for gene from tracking file. However best answer can come from Cole (who is now at Broad Institute) if he can bring is some insight what these millions of files mean and how to answer the question with which someone start RNA-seq experiment.

Last edited by honey; 05-01-2011 at 04:46 AM.
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