Hi all,
I read one paper "Differential gene and transcript expression analysis of 
RNA-seq experiments with TopHat and Cufflinks".
They say the procedure for RNA-Seq analysis is 
Tophat-->cufflinks-->cuffmerge-->cuffdiff
 
But what I normally do in Galaxy is 
Tophat-->cufflinks-->cuffcompare-->cuffdiff. I have six samples, which means I 
will generate 6 assembled transcript files by cufflinks. Then I run cuffcompare 
using all six assembled transcript files as input. The resulting "combined 
transcript" is the input for cufflinks.
 
I don't know why I shoud use cuffmerge. Actually I don't understand the 
function of cuffmerge.
 
Did I miss something??
Please let me know your opinions.
Jiwen
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