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
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.
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