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