Hello, 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 --- 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 -----------------------------------------------------------------------
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