I am new in using Galaxy and I am working on .bam files generated by our 
sequencing platform, using the LifeScope software associated to ABI 5500 
sequencer. I uploaded my files on a galaxy browser ( 
http://galaxy.raetschlab.org) and I tried to run cufflink assemble and quantify 
reads expression levels for each file. However, when I run cufflinks (using 
default parameters) the output is an empty file.
What is going wrong? Should I use special parameters? Are the .bam files 
generated by LifeScope suitable for cufflink analysis or should I transform the 
xsq ABI output in a fastq and then apply TopHat?

I thank you very much for your help


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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