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Old 07-04-2014, 10:38 AM   #2
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Location: Montreal

Join Date: May 2013
Posts: 367

These are vast questions.
I don't have time to answer them fully, but here are some tips, which I hope you will find helpful.

If you're willing to use some R commands, you might want to try CummeRbund for the downstream analysis.
It's not the greatest software, but it does it make it easier to extract more information out of all the data.

I'm not sure why you want to remove isoforms with an FPKM out of 0. An FPKM of 0 means that the isoform is either not expressed, or so lowly expressed that it cannot be detected at this sequencing depth. This is useful information, so I would not remove it.
blancha is offline   Reply With Quote