Wei, The best way to move individual datasets b/t Galaxy instances is by link: right click on the dataset's save icon (a disk), copy the link, and paste that into the upload form. A couple word of caution about our test server: it is experimental and may be nonfunctional or unavailable periodically, there is little/no support is offered for new tools, and quotas are quite low. For analyses that require multiple steps, test most likely will not meet your needs. Finally, please always cc the mailing list when replying. Good luck, J. On Jan 9, 2012, at 7:48 PM, Wei Liao wrote:

Hi, Jeremy, Thank you for your help，I will try to use pileup tool. I noticed that there are many great tools I am interested on the test server such as GATK, however, all my data are on main server and the bam files are huge (5-7GB), do you know a fast way to transfer data from main server account to test server?

Wei It

On Mon, Jan 9, 2012 at 10:40 AM, Jeremy Goecks <jeremy.goecks@emory.edu> wrote: Wei,

The pileup tool will help you find SNPs in your data; you'll want to read the documentation to understand how best to use it for your needs. You can also try the Unified Genotyper on our test server ( http://test.g2.bx.psu.edu/ ), but it's in alpha/beta status and we aren't providing any support for it yet.

Good luck, J.

On Jan 9, 2012, at 1:28 AM, <ericliaowei@gmail.com> <ericliaowei@gmail.com> wrote:

...

HI, I am new to the RNA-seq, and the only available sources for me to do analysis is the Galaxy server. I want find out SNP and point mutations in RNA-Seq data using Galaxy (I do not know if anyone using RNA-seq data to find point mutations, because there is whole Genome sequencing for reporting mutations and SNPs). I have been searching in the forum for a step-by-step protocols for doing it, but could not find it. I have one normal sample and two cancer samples, a TopHat produced "accepted Hits.bam" file for each one. I want to find out SNP and point mutations in the cancer samples, so How do I go from here? Can anyone show me how to do it in Galaxy main server? Thanks!

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-- Wei Liao Research Scientist, Brentwood Biomedical Research Institute 16111 Plummer St. Bldg 7, Rm D-122 Sepulveda, CA 91343 818-891-7711 ext 7645