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Old 05-09-2016, 03:27 AM   #1
Renshin
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Default Statistic on FPKMs of gene in one condition

Hello,

With the help of cufflinks; I calculated the number of FPKM for each contigs. In my study, I don't want to know which genes are expressed differently according to the conditions. I just want to know which ones are the most expressed. What program can I use or statistic?

Thank you for you help
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Old 05-09-2016, 06:45 AM   #2
dpryan
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If you already have FPKMs then you already have your answer. The FPKM is the metric, just use the highest X%.
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Old 05-09-2016, 08:59 AM   #3
Renshin
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I have perhaps statistically classify the FPKMs , it could be interesting. No ?
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Old 05-09-2016, 12:52 PM   #4
dpryan
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You can use a method like zFPKM if you need something other than top X%, but that's not what you mentioned in your first post.
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Old 05-09-2016, 01:34 PM   #5
Renshin
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Thank you, very interesting. I'm researching of ideas for my study on the FPKMs. I'm open to ideas.
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Old 05-12-2016, 09:23 AM   #6
Renshin
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I calculated the zFPKM, but I don't calculate the treshold because I don't have a file containing the results of chromatin state analysis. Moreover, i work about an insect, i can't use threshold de -3 for human.

Can you help me
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