Hi Ateequr, I sent you a reply for this question when you asked me directly last week, but perhaps this got missed. The mapping step for you data is OK. The problem comes up when Cufflinks is used with the bacterial (circular) genome with your current parameter settings. As I mentioned, there has been some limited discussion about RNA-seq tools and parameters for circular genomes on this mailing list, but we recommended seqanswers.com or the tool authors as the best resources for this specific type of analysis advice. To search prior Q/A on a Galaxy mailing list: http://galaxy.psu.edu/search/mailinglists/ To reach the tool authors: tophat.cufflinks@gmail.com http://cufflinks.cbcb.umd.edu http://cufflinks.cbcb.umd.edu/faq.html Others are also welcomed to offer more advice directly as replies to this thread, Best wishes for your project, Jen Galaxy team On 3/2/12 6:57 AM, Ateequr Rehman wrote:

Dear Galxy admin and user

I have generated BAM file from my RNa seq data by using Bowtie with custom reference, followed by Filter SAM and SAM to BAM connversion, i wish to run cufflink, but its just givinbg me emty file, any suggestion, how to proceed Ateequr Rehman House No. 2 ground floor Blauenstr. 10 79115 Freiburg im Breisgau

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