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-datasetscuffl...). 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...) or cuffcompare (see https://main.g2.bx.psu.edu/u/davide-degliesposti/h/rna-seqtest-datasetsjan-2...) 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 ----------------------------------------------------------------------- This message and its attachments are strictly confidential. If you are not the intended recipient of this message, please immediately notify the sender and delete it. Since its integrity cannot be guaranteed, its content cannot involve the sender's responsibility. Any misuse, any disclosure or publication of its content, either whole or partial, is prohibited, exception made of formally approved use -----------------------------------------------------------------------