Hi Thanh,

Did the Tuxedo suite not work out for you in the end? Or the other tools that Ross suggested? These are both pipelines that are in common use.
http://lists.bx.psu.edu/pipermail/galaxy-user/2013-July/006367.html

Using a cloud Galaxy and installing tools from the Tool Shed is required for certain tools, perhaps that is the problem? Many tools now have automatic dependency installation, making set-up much easier. For a demonstration, watch the Channel: Galaxy ToolShed videos at Vimeo:
http://vimeo.com/user20484153

You also may want to look at some of the miRNA specific tools in the Tool Shed. They can be found under "Sequence Analysis". Most of these have online documentation, or the tool author includes documentation, that you can review to see if the tool is a good fit for what you want to do (if it is not expression analysis anymore, or you want to try something different like DESeq).
http://toolshed.g2.bx.psu.edu/repository

Hopefully this helps,

Jen
Galaxy team

On 9/18/13 10:19 AM, Hoang, Thanh wrote:

Hi all,

I would like to analyze my miRNA sequencing analysis from mouse tissue. I have not any idea which tools or pipeline work best. Do you have any suggestion?

Regards

Thanh

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