Hello Kanwar,

If you want to use a microbial genome, it can be used as a custom reference genome in Galaxy the same as any other reference genome, with Bowtie or TopHat. Instructions are at this wiki:
http://wiki.g2.bx.psu.edu/Support#Custom_reference_genome

To index the data and use in a local instance, you will want to create the indexes on the command line. Follow the instructions in our admin wiki:
http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup

The above are technical set-up. There are still scientific considerations. Reviewing the RNA-seq pipeline's manuals, researching Q/A on message boards such as seqanswers.com, and perhaps contacting the tool authors would be strongly recommended to determine if this is the appropriate tool set for your purposes:
http://tophat.cbcb.umd.edu/
http://cufflinks.cbcb.umd.edu/
tophat.cufflinks@gmail.com

Best,

Jen
Galaxy team

On 6/26/12 7:36 AM, shamsher jagat wrote:

I was wondering if it is some how possible in galaxy to format FAST genome seq file of microbial genome to format to generate bowtie index so that it can be used for RNA seq analysis using TopHat. Alternatively any pointer to an available tool which can generate index files.

Thanks

Kanwar
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