Cuffmerge does some additional steps that Cuffcompare does not; specifically, Cuffmerge attempts to remove assembly artifacts: http://cufflinks.cbcb.umd.edu/manual.html#cuffmerge It's likely that the (presumed) artifacts removed by Cuffmerge account for the differences that you're seeing.

Best,
J.

On Apr 5, 2013, at 8:33 AM, Davide Degli Esposti wrote:

Dear Galaxy team,

I have a question about RNA analysis with the cufflinks package.

I have some bam files to analyze from a SOLiD platform. Some previous tests show that these bam/sam files are different from those coming from Tophat and cufflinks cannot assemble them using a reference annotation (XS attribute lacking in spliced alignments). (see https://main.g2.bx.psu.edu/u/davide-degliesposti/h/rna-seqtest-datasetscufflinks). An apparent solution is to include the reference annotation in the cuffmerge (see  https://main.g2.bx.psu.edu/u/davide-degliesposti/h/rna-seqtest-datasetsapril-20132) or cuffcompare (see https://main.g2.bx.psu.edu/u/davide-degliesposti/h/rna-seqtest-datasetsjan-2013-1) steps. Doing like this allowed me to run cuffdiff on my datasets without apparent technical errors. However, when I compare the list of differentially expressed transcripts (DETs), these results extremely different: using cuffcompare, I got 390 DETs and using cuffmerge I got 770 DETs, but just 60 genes are shared between the two lists. The parameters used in cuffdiff (FDR, Min Alignement counts, etc.) are the same for the two analyses.

Do you have any explanation about that? I expected that cuffcompare and cuffmerge did not lead to outputs quantitatively different. Where may the source of this difference be?

I thank you for your cooperation

Davide
---
Davide Degli Esposti, PhD
Epigenetic (EGE) Group
International Agency for Research on Cancer
Tel. +33 4 72738036
Fax. +33 4 72738322
150, cours Albert Thomas
69372 Lyon Cedex 08
France 






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