I'm new to RNA-Seq analysis and think this question must have been asked
before, but I can't find an answer in the Galaxy-user or Seq-answers

My question is, if I use the public Galaxy server interface to TopHat and
Cufflinks, is there any access to "cuffmerge"?

Also, I'm trying to understand the difference between using cuffmerge and
then using cuffcompare (without a reference genome) to assemble gtf
transcript files produced by Cufflinks for each group of 3 Illumina
paired-end reads corresponding to biological replicates, in order to use the
resulting combined gtf file for comparing the TopHat alignments of two such
groups using cuffdiff.

Is there any difference in the output between cuffdiff and cuffcompare,
using in this fashion?  For example, do they form the "union" of transcripts
by the same rules, and do their outputs contain (or lack) the same columns
(strand, perhaps??)  I've read things on seq-answers indicating that I
should be using cuffmerge, but I can't find it on the public server and
apparently haven't installed it properly on my own computer so far.
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