Hi Thanh,
This is due to Cuffdiff correcting for the size of smaller transcripts, the
authors call it the effective length correction. It is supposed to
correct the loss of shorter transcripts upon size selection in creating
your RNA-seq library. The default setting on Galaxy is to use the
Hi, Thanh,
If your primary goal is inference about differential 'gene' expression
taking biological variability into account with biological replicates for
each of two conditions, you might want (eg see Dillies et al.,
http://bib.oxfordjournals.org/content/early/2012/09/15/bib.bbs046.long and
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