In the Cufflinks manual (http://cole-trapnell-lab.github.io/cufflinks/cufflinks/#advanced-abundance-estimation-options) it says to use this command: -N/–upper-quartile-norm
In the Cuffdiff manual (http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/#library-normalization-methods) it says to use this command: --library-norm-method quartile. It also says there that the quartile normalization method is not supported by Cufflinks but only by Cuffdiff (which implies that its not just that a different command is used in Cufflinks but that the method as whole is not available for Cufflinks options).
I would appreciate a clarification, as to whether it may in fact work for Cufflinks but just uses different command, -N/–upper-quartile-norm, which is also not supposed to be used for this normalization for the Cuffdiff?
If both, Cufflinks and Cuffdiff, work with the upper-quartile normalization, then which combination of the options is appropriate for the classical upper-quartile normalization described in the literature? I would assume to use it only in Cufflinks but not in Cuffdiff, and if it really is not available for Cufflinks, then it is not the classical upper-quartile normalization (see under a different posting why I would think that https://www.biostars.org/p/195489/#195507).