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Old 04-10-2012, 11:24 PM   #1
m_elena_bioinfo
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Location: Ospedali Riuniti di Bergamo, ITALY

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Default RNASeq

Dear,
anyone could help me to "understand" the outputs of cufflinks?
How can I use these data and FPKM values to extract the differential gene expression and the different abundance of isoforms?

Moreover, where can I find a gtf annotation file for human to integrate in the run of cufflinks as -g parameter?

thanks a lot
ME
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Old 04-11-2012, 12:33 AM   #2
mixter
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Hi,

There's a verbose description of each column under http://cufflinks.cbcb.umd.edu/manual...uffcomp_output

Also, in my experience, for a lot of technical questions and concerns the FAQ is helpful, http://cufflinks.cbcb.umd.edu/faq.html
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