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Old 10-20-2013, 02:48 AM   #1
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Default Cuffdiff 2.1.1 normalization

I used cuffdiff 2.1.1 with the default geometric normalization, which should not consider the transcripts' length but only the geometric mean of number of counts per sample (as DESeq does).
If this is so, I don't understand the meaning of 2 other optional parameters:

--no-effective-length-correction: "Cufflinks will not employ its "effective" length normalization to transcript FPKM"
--no-length-correction: "Cufflinks will not normalize fragment counts by transcript length at all (??). Use this option when fragment count is independent of the size of the features being quantified (e.g. for small RNA libraries, where no fragmentation takes place, or 3 prime end sequencing, where sampled RNA fragments are all essentially the same length). Experimental option, use with caution".

Can anyone tell the difference between these 2 options, and why are they needed if the geometric mean normalization does not consider the length anyway?
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