Dear Sir or Madam,
I am planning to do clustering of several libraries based on the output of
cuffcompare or cuffdiff, as they allow me to construct a matrix whose columns
represent the libraries and rows are the count of transcripts or genes. I want
to construct the matrix because it is the
1. It seems that it is better to run everything up to cuffdiff, but does
cuffdiff allow multiple sample comparison because I read somewhere that even
for multi-samples it still compare tham pairwisely?
Cuffdiff supports replicate analysis.
In a sense, because I want to do clustering which
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