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
 An apparent solution is to include the reference annotation in the cuffmerge 
 or cuffcompare (see
 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 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

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